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Table 4 Lead SNPs in secondary analyses

From: A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts

ALSPAC 6–9-year-olds (N = 3647)

 

rsID

Cluster

chr:pos_nonEA_EA

β (SE)

P

β (SE)

P (proxy)

Location

Nearby genes

Lead SNP locus (or distance to genes within 200 kb, in bp)

β (SE)

P (CC)a

β (SE)

P (MA1)

β (SE)

P (MA2)

rs139045492

20:22836201-22836202

20:22836202_G_A

− 0.695 (0.119)

p = 6.35E−09

–

Intergenic

.

SSTR4 (dist = 179,855)

− 0.489 (0.240)

p = 0.042

0.080 (0.078)

p = 0.306

− 0.005 (0.097)

p = 0.956

rs144874692

3:175689046-175689047

3:175689047_G_A

− 0.632 (0.112)

p = 1.78E−08

− 0.328 (0.105)

p = 0.002

Intergenic

.

NAALADL2 (dist = 165,619)

− 0.024 (0.263)

p = 0.926

Proxy:

0.00 (0.075)

p = 1.00

Proxy:

0.016 (0.094)

p = 0.861

ALSPAC neonates (N = 2102)

rsID

Cluster

chr:pos_nonEA_EA

β (SE)

P

β (SE)

P (Proxy)

Location

Nearby genes

Lead SNP locus (or distance to genes within 200 kb, in bp)

β (SE)

P (CC)a

β (SE)

P (MA1)

β (SE)

P (MA2)

rs10424198

19:17354824-17461934

19:17409671_C_T

− 0.262 (0.034)

p = 1.40E−14

–

Intronic

ABHD8, ANKLE1, ANO8, BABAM1, DDA1, GTPBP3, MRPL34, NR2F6, PLVAP, USHBP1

ABHD8

− 0.326 (0.193)

p = 0.095

− 0.010 (0.017)

p = 0.556

0.002 (0.022)

p = 0.911

UKBS (males) (N = 1333)

rsID

Cluster

chr:pos_nonEA_EA

β (SE)

P

β (SE)

P (Proxy)

Location

Nearby genes

Lead SNP locus (or distance to genes within 200 kb, in bp)

β (SE)

P (CC)

β (SE)

P (MA1)

β (SE)

P (MA2)

rs11687359

2:1969703-1969704

2:1969704_G_A

0.401 (0.078)

p = 2.94e−07

–

Intronic

MYT1L

MYT1L

0.362 (0.080)

p = 6.52e−06

0.006 (0.032)

p = 0.845

0.043 (0.041)

p = 0.286

rs13070764

3:73309902-73310337

3:73309903_G_A

− 0.497 (0.099)

p = 5.84e−07

–

Intergenic

.

PPP4R2 (dist = 194,892), PDZRN3 (dist = 121,678)

− 0.509 (0.100)

p = 4.15e−07

0.100 (0.043)

p = 0.020

0.098 (0.060)

p = 0.101

  1. Abbreviations: rsID SNP identifier; chr:pos_nonEA_EA chromosome, position, non-effect allele, effect allele; bp base pairs; β regression coefficient (additive model); SE standard error; P p value; P (Proxy) p value (for a proxy SNP, rs144928561, r2 = 0.29); P (CC) p value (cell-proportion adjusted analysis); P (MA1) pvalue (‘Meta-analysis 1’, 6799 adult females); p value (MA2) P (‘Meta-analysis 2’, 4743 females with DNA from white cells)
  2. aNB large drop in power for ALSPAC mothers (see Table 1)