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Table S3 PCMs covered by the Denisovan sequence but not the Neanderthal sequence

From: Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

Acc Chr Location Strand Tag Disease Gene Mutation AA seq Type
CM062419 chr1 19483828 - DP Leukaemia, risk,
association with
AKR7A3 C > T:CT Asp-Asn Denisovan
CM098300 chr1 24074507 - DFP Eating disorders,
association with
CNR2 T > C:CC Gln-Arg Ancestral
CM066774 chr1 110267989 + DP Periodontitis,
association with?
CSF1 T > C:CC Leu-Pro Ancestral
CM094244 chr1 111656412 + FP Increased enzyme
activity, association
with?
CHIA A > G:GA Asn-Asp Derived
CM094243 chr1 111656461 + DFP Asthma, protection
against, association
with?
CHIA G > T:TG Arg-Met Derived
CM084968 chr1 150552554 - DP Psoriasis, increased
risk, association with
FLG G > A:AG Pro-Ser Derived
CM067657 chr1 156591049 + DP Guillain-Barré
syndrome, reduced
risk, association with
CD1E A > G:GG Gln-Arg Ancestral
CM033904 chr1 169444714 + FP Flavin-containing
monooxygenase 2
(FMO2) gene variant
FMO2 T > C:CC Term-Gln Ancestral
CM043273 chr1 195670491 + DM Retinitis pigmentosa CRB1 G > A:AG Gly-Ser Derived
CM024366 chr1 224093029 + DFP Preeclampsia,
association with
EPHX1 A > G:GA His-Arg Derived
CM994344 chr10 115795046 + FP Gain of function,
association with
ADRB1 G > C:CC Gly-Arg Ancestral
CM067436 chr11 7020956 + DM Spermatogenic
failure
NLRP14 G > A:AG Ala-Thr Derived
CM043536 chr11 47326617 - DM Cardiomyopathy,
hypertrophic?
MYBPC3 T > C:CT Ser-Gly Derived
CM035848 chr11 57739196 + FP Olfactory receptor
deficiency?
OR1S1 G > A:GA Arg-His Denisovan
CM087504 chr11 102218830 - DP Blood pressure,
association with
MMP3 T > C:CC Lys-Glu Ancestral
CM041241 chr11 112776038 + FP Reduced dopamine
D2 receptor
(DRD2) receptor
density, association
with?
ANKK1 G > A:AA Glu-Lys Ancestral
CM082943 chr11 118720796 - DM Primary
angle-closure
glaucoma?
MFRP C > T:TT Arg-His Ancestral
CM075018 chr11 130255852 - DP Coronary heart
disease, association
with
SNX19 A > C:CC Leu-Arg Ancestral
CM091988 chr12 32913201 - DM Arrhythmogenic
right ventricular
cardiomyopathy
PKP2 A > G:GG Leu-Pro Ancestral
CM087618 chr12 56152088 + DFP Inflammatory bowel
disease, association
with
GLI1 G > C:CC Glu-Gln Ancestral
CM098354 chr12 120099486 + FP Altered function,
association with
P2RX7 G > A:AA Ala-Thr Ancestral
CM065186 chr13 38162690 + DP Colorectal cancer,
increased risk,
association with
FREM2 T > C:CC Phe-Ser Ancestral
CM063919 chr13 45546095 - FP Higher
thrombin-activatable
fibrinolysis inhibitor
(TAFI) antigen levels,
association with
CPB2 C > T:TT Ala-Thr Ancestral
CM044579 chr13 51413355 - DM Wilson disease? ATP7B A > G:GG Val-Ala Ancestral
CM063843 chr14 19994994 + DFP Amyotrophic lateral
sclerosis, association
with
APEX1 T > G:GG Asp-Glu Ancestral
CM073244 chr14 20010446 + DP Faster cognitive
decline in
Alzheimer's disease,
association with
NP G > A:AG Gly-Ser Derived
CM068495 chr15 49316404 - DP Increased cortical
bone mass density,
association with
CYP19A1 T > C:CC Val-Val Ancestral
CM045806 chr15 83248435 + FP Reduced affinity for
gemcitabine,
association with
SLC28A1 G > A:AG Val-Ile Derived
CM102885 chr16 10908349 + DP Multiple sclerosis,
increased risk,
association with
CIITA G > C:CC Gly-Ala Ancestral
CM093131 chr16 55950234 + DP Helicobacter
pylori-related gastric
carcinoma,
association with
CCL22 A > C:CC Asp-Ala Ancestral
CM067679 chr17 7858004 + DP Lung cancer,
susceptibility to,
association with
GUCY2D T > A:AA Leu-His Ancestral
CM073339 chr17 24310977 - DM Febrile seizures? SEZ6 T > C:CC Thr-Ala Ancestral
CM057951 chr17 37960432 + DP Endometriosis,
association with
HSD17B1 A > G:AG Ser-Gly Denisovan
CM994214 chr17 39808591 - DP Reduced post-stroke
mortality, association
with
ITGA2B A > C:GC Ile-Ser Unsure
CM091892 chr17 42363569 + DP Hypertension,
association with
GOSR2 G > A:AG Arg-Lys Derived
CM091876 chr17 73642170 + DP Epidermodysplasia
verruciformis,
susceptibility in HIV,
association with
TMC8 A > T:TA Asn-Ile Derived
CM000831 chr19 3546794 - DP Bronchial asthma,
association with
TBXA2R A > G:GG Tyr-Tyr Ancestral
CM030470 chr19 18041451 - DP Tuberculosis,
susceptibility to,
association with
IL12RB1 A > G:GG Met-Thr Ancestral
CM044082 chr19 18407678 - DP Spina bifida, reduced
risk, association with
isyna1 T > C:CC Leu-Leu Ancestral
CM057586 chr19 40534926 + DP Increased beta-cell
function, association
with
FFAR1 G > A:AA Arg-His Ancestral
CM057545 chr19 50560149 - DP Lung adenocarcinoma,
increased risk,
association with
ERCC2 G > T:GT Arg-Arg Denisovan
CM044227 chr19 60088712 + DP Aggressive
periodontitis,
reduced risk, assoc
with
FCAR A > G:GG Arg-Arg Ancestral
CM003809 chr2 38155681 - DP Breast or lung
cancer, association
with
CYP1B1 C > A:AA Ala-Ser Ancestral
CM101950 chr2 98363138 + DM Progressive cone
dystrophy?
CNGA3 C > T:TC Pro-Leu Derived
CM092797 chr2 169550992 - FP Alternate splicing,
association with
ABCB11 T > C:CT Gly-Gly Derived
CM066575 chr2 218738088 - DP AIDS progression,
protection,
association with
IL8RA A > C:CC Met-Arg Ancestral
CM057769 chr2 234266408 + FP Altered enzyme
activity, association
with
UGT1A6 T > G:GG Ser-Ala Ancestral
CM910018 chr2 241466189 + DP Hyperoxaluria,
association with
AGXT A > G:GG Ile-Met Ancestral
CM053304 chr20 54257212 + DP Obesity, association
with
MC3R C > A:AA Thr-Lys Ancestral
CM970391 chr22 18331207 + DFP Schizoaffective
disorder, association
with
COMT C > G:GG Leu-Leu Ancestral
CM961335 chr22 30817700 + DM Glucose/galactose
malabsorption
SLC5A1 G > A:AA Ala-Thr Ancestral
CM930187 chr22 40853887 - DP Parkinson's disease,
association with
CYP2D6 G > A:GA Arg-Cys Denisovan
CM099899 chr22 41888870 + FP Increased
pregnenolone levels,
association with
TSPO A > G:GG Thr-Ala Ancestral
CM025430 chr4 2975841 + FP Activity, association
with
GRK4 C > T:TT Ala-Val Ancestral
CM013959 chr4 23424760 - DP Diabetes, type 2,
association with
PPARGC1A C > T:TC Gly-Ser Derived
CM033593 chr4 100479812 - DP Alcoholism,
increased risk,
association with?
ADH1C T > C:CC Ile-Val Ancestral
CM064956 chr4 109893565 - DP Colorectal cancer,
increased risk,
association with
AGXT2L1 A > G:GG Ser-Pro Ancestral
CM030066 chr4 149576925 - FP Reduced expression,
association with
NR3C2 T > C:TC Ile-Val Denisovan
CM080365 chr4 155711209 + DP Increased clot
stiffness, association
with
FGB G > A:AA Arg-Lys Ancestral
CM057405 chr4 156355126 + DP Severe obesity, in
men, association
with
NPY2R C > T:TT Ile-Ile Ancestral
CM067358 chr5 22114341 - DP Lung cancer,
susceptibility to,
association with
CDH12 C > T:TT Val-Met Ancestral
CM094788 chr5 121441107 - DFP Breast cancer,
increased risk, in
African American
women, association
with
LOX C > T:TT Arg-Gln Ancestral
CM013815 chr5 147461148 + DP Atopy, maternally
inherited,
association with
SPINK5 G > A:GA Glu-Lys Denisovan
CM083577 chr6 24611569 + DFP Impaired cognitive
function, association
with
ALDH5A1 C > T:TT His-Tyr Ancestral
CM086146 chr6 25921129 - DP Uric acid
concentration,
association with
SLC17A1 G > A:AA Thr-Ile Ancestral
CM052232 chr6 80683094 - DP Age-related
maculopathy,
association with
ELOVL4 T > C:CT Met-Val Derived
CM073245 chr7 34784638 + DP Panic disorder, in
males, association
with
NPSR1 A > T:TT Asn-Ile Ancestral
CM084696 chr7 87017537 - DFP Parkinson's disease,
association with
ABCB1 A > G:GG Gly-Gly Ancestral
CM091200 chr7 129737976 + DP Prostate cancer,
aggressive
early-onset,
association with
CPA4 G > T:TT Gly-Cys Ancestral
CM952203 chr7 142350235 - FP Kell blood group
variation
KEL A > G:GA Leu-Pro Derived
CM073993 chr7 150188598 + FP Reduced activity,
association with
ABP1 C > G:GG His-Asp Ancestral
CM973386 chr8 18124281 + FP Increased activity,
association with
NAT1 G > A:AG Val-Ile Derived
CM099895 chr8 24412708 + DP Schizophrenia,
association with
ADAM7 A > C:CC Asn-His Ancestral
CM064954 chr8 26683945 - DP Hypertension,
association with?
ADRA1A A > G:GG Cys-Arg Ancestral
CM033767 chr8 27414422 + DFP Coronary heart
disease, in
Caucasians,
association with
EPHX2 A > G:GA Lys-Arg Derived
CM034886 chr8 91059655 - DP Lung cancer,
association with?
NBN C > G:GG Glu-Gln Ancestral
CM045665 chr8 120033233 - DP Osteoporotic
fractures, association
with
TNFRSF11B G > C:CG Asn-Lys Derived
CM093465 chr9 2181309 + DFP Schizophrenia,
association with
SMARCA2 C > G:GC Asp-Glu Derived
CM073190 chrX 43475980 + DP Bipolar disorder,
association with?
MAOA T > G:TG Arg-Arg Denisovan
CR072321 chr1 11841858 - DFP Diabetes, type, 2,
reduced risk,
association with
NPPB A > G:GG   Ancestral
CR080762 chr1 15645754 + DM Pancreatitis, chronic? CTRC T > C:CC   Ancestral
CR080761 chr1 15645757 + DM Pancreatitis, chronic? CTRC A > G:GG   Ancestral
CR016187 chr1 87101113 - FP Increased
selenocysteine
insertion sequence
(SECIS) efficiency,
association with
sep15 C > T:TT   Ancestral
CR092707 chr1 201194130 - DFP Lower insulin
resistance,
association with
ADIPOR1 C > T:TT   Ancestral
CR034628 chr10 26545502 + DP Obesity, association
with?
GAD2 G > A:GA   Denisovan
CR061340 chr11 35397552 - DFP Progressing stroke,
increased risk,
association with
SLC1A2 T > G:GG   Ancestral
CR068212 chr11 59612604 + DFP Asthma,
aspirin-intolerant
MS4A2 T > C:CC   Ancestral
CR063407 chr14 50069895 - DP Diabetes, type 2,
reduced risk,
association with
MAP4K5 G > A:AA   Ancestral
CR077666 chr15 71712835 - DFP Schizophrenia,
reduced risk,
association with?
NPTN C > A:CA   Denisovan
CR084880 chr17 35697157 + DFP Hepatocellular
carcinoma, reduced
risk, association with
CDC6 A > G:GG   Ancestral
CR087465 chr17 39785770 + DFP Frontotemporal
dementia,
association with
GRN C > T:TT   Ancestral
CR035036 chr18 647685 + FP Transcriptional
activity, association
with
TYMS G > C:CC   Ancestral
CR032436 chr18 45342041 + DP High-density
lipoprotein (HDL)
cholesterol levels,
association with?
LIPG A > C:CA   Derived
CR087182 chr19 44589133 + DFP Rheumatoid
arthritis, shorter
duration, association
with
ZFP36 A > G:GG   Ancestral
CR035033 chr19 46188301 + FP Cytochrome P-450
(CYP) 2B6
expression,
association with?
CYP2B6 T > C:CC   Ancestral
CR068525 chr2 69467665 - DFP Diabetes, type 2,
association with
GFPT1 A > G:GG   Ancestral
CR077669 chr2 85748849 - FP Increased promoter
activity, association
with
SFTPB T > G:GG   Ancestral
CR093507 chr2 168743982 - DFP Hypertension,
association with
STK39 A > G:GG   Ancestral
CR093026 chr2 169465787 + DFP Increased insulin
secretion,
association with
G6PC2 G > A:AA   Ancestral
CR073559 chr2 224174588 - DFP Hypertension,
association with
SCG2 C > T:TT   Ancestral
CR053505 chr20 4653756 + DP Creutzfeldt-Jakob
disease, association
with?
PRND T > C:CC   Ancestral
CR015272 chr22 40858326 - FP Intermediate
metaboliser,
association with?
CYP2D6 C > G:GG   Ancestral
CR055620 chr4 75938792 - FP Promoter activity,
association with
BTC C > G:GG   Ancestral
CR093469 chr6 2945302 + DFP Breast cancer,
decreased risk,
association with
NQO2 A > C:CA   Derived
CR035882 chr6 78230101 - DFP Suicidal ideation, in
major depression,
association with
HTR1B A > C:CA   Derived
CR025333 chr6 137582213 - DFP Malaria,
susceptibility,
association with
IFNGR1 A > G:GG   Ancestral
CR093919 chr6 153121754 + DP Pulmonary arterial
hypertension,
idiopathic,
association with?
VIP T > C:CC   Ancestral
CR016149 chr7 22732746 + FP Altered
transcriptional
activity, association
with
IL6 A > G:GG   Ancestral
CR053504 chr7 91995822 - FP Gene expression,
association with
PEX1 A > G:GA   Derived
CR041138 chr7 99192235 - DP Prostate cancer, low
aggressiveness,
association with
CYP3A4 G > A:AG   Derived
CR072316 chr7 128376663 + FP Shorter transcript,
association with
IRF5 G > A:AA   Ancestral
CR962526 chr8 41774321 - DM Spherocytosis ANK1 A > G:GA   Derived
CR098013 chr9 22109195 + DFP Coronary artery
disease, association
with
CDKN2BAS C > T:CT   Denisovan
CR044772 chr9 99499399 - DP Lung adenocarcinoma,
risk, association with
XPA T > C:CC   Ancestral
CR020828 chr9 106730356 - DP Reduced risk of
coronary artery
disease, association
with
ABCA1 G > C:CC   Ancestral
CR052068 chr9 136911887 + FP Promoter activity,
association with
FCN2 A > G:GG   Ancestral
CR042847 chr9 138995962 + DP HDL cholesterol,
association with?
PTGDS A > C:CC   Ancestral