Table 2 Summary of transcriptomic studies for loci associated with epigenetic age acceleration

From: GWAS of epigenetic aging rates in blood reveals a critical role for TERT

  

Meta GWAS

cis-eQTL

SMR

Band

SNP

P-value (sign)

Database

Gene

P-value (sign)

P-value (sign)

IEAA

3q25.33

rs11706810

1.6 × 10–9 (+)

FHS

KPNA4

4.2 × 10–23 (+)

5.1 × 10−5 (+)

6p22.3

rs6915893

1.6 × 10–13 (+)

FHS

TPMT

6.0 × 10–14 (+)

1.1 × 10−7 (+)

   

GTEx

 

1.5 × 10–4* (+)

2.2 × 10−6 (+)

   

LSMeta

 

2.3 × 10–27 (+)

3.5 × 10−7 (+)

17q22

rs78781855

5.6 × 10–9 (–)

FHS

STXBP4

1.0 × 10–88 (–)

6.2 × 10−4 (+)

EEAA

4p16.3

rs2341303a

6.5 × 10–11 (–)

LSMeta

RNF4

1.6 × 10–10 (–)

2.0 × 10−3 (+)

10p11.21

rs71007656

7.5 × 10–11 (+)

FHS

ZNF25

7.9 × 10–7 (+)

2.8 × 10−3 (+)

   

GTEx

HSD17B7P2

3.0 × 10–8 (+)

6.9 × 10−6 (+)b

10p11.1

rs1005277

1.2 × 10–13 (+)

GTEx

HSD17B7P2

1.1 × 10–5 (+)

6.9 × 10−6 (+)b

  1. Bands corresponding the position of Meta GWAS SNP
  2. The table presents a total of six cis genes highlighted from transcriptomic study using three large-scale databases (N = 10,906), including (1) FHS (N = 5257), (2) GTEx (N = 338), and (3) LSMeta (5311). Each cis gene exhibited significant cis-eQTL with several nearby GWAS SNPs at FDR q < 0.05 in at least one study and also showed a significant pleiotropic association in SMR analysis at P < 0.05 after Bonferroni correction. For each gene, we list the unadjusted P-values (sign) from Meta GWAS for IEAA (or EEAA), cis-eQTL and SMR analysis. The column (sign) indicates the sign of Z-statistic at each test while the test alleles were converted to the same alleles (with minor variants) for both Meta GWAS and cis-eQTL tests. The summary statistics of Meta GWAS and cis-eQTL are both based on the leading marker with the most significant P-value in a given locus, according to the GWAS results
  3. * FDR > 0.05 but FDR < 0.05 associated with other GWAS SNPs (Supplementary Data 3)
  4. a The SNP rs2341303 is a surrogate of the leading marker rs10937913 in 4p16.3 (LD \(r_{{\rm EUR}}^2\) = 0.98)
  5. b The SMR results are derived from the same model as the analysis used the cis SNPs of the gene HSD17B7P2
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