Table 3

The hub SNPs/genes identified in the top-ranked 1000 SNP pairs

Hub SNPs from analyses of complete SNP set


Disease

Hub SNPs (Genomic position)

# Interacting SNPs


BD

rs1553460 (Chr4:17804959)

1000


CAD

rs3785579 (Chr17:62472963)

1000


CD

rs1553460 (Chr4:17804959)

978


rs4471699 (Chr16:30227808)

22


HT

rs10843660 (Chr12:30259724)

999


RA

rs3785579 (Chr17:62472963)

1000


T1D

rs9273363 (Chr6:32734250)

1000


T2D

rs7077039 (Chr10:114779067)

833


rs10787472 (Chr10:114771287)

54


rs11196208 (Chr10:114801306)

39


rs11196205 (Chr10:114797037)

30


rs10885409 (Chr10:114798062)

22


rs4074720 (Chr10:114738487)

17


Hub genes from gene-only SNP analyses


Disease

Hub genes

# Interacting genes


BD

CENPN: centromere protein N

653


CAD

CACNG1: calcium channel, voltage-dependent, gamma subunit 1

709


CD

ATG16L1: ATG16 autophagy related 16-like 1 (S. cerevisiae)***

256


IL23R: interleukin 23 receptor ***

20


HT

tcag7.23: similar to ribosomal protein L18; 60S ribosomal protein L18

170


BCAT1: branched chain aminotransferase 1, cytosolic ***

57


SAMD4A: sterile alpha motif domain containing 4A *

27


GAB1: GRB2-associated binding protein 1 *

25


RHOJ: ras homolog gene family, member J

20


LYPD5: LY6/PLAUR domain containing 5 *

12


RA

CACNG1: calcium channel, voltage-dependent, gamma subunit 1

676


T1D

HLA-DQB1: major histocompatibility complex, class II, DQ beta 1**

686


T2D

TCF7L2: transcription factor 7-like 2 (T-cell specific, HMG-box)***

481


* Genes associated with disease SNPs that were previously reported in WTCCC original paper

** Genes previously reported to be disease-associated in HuGE Navigator database

*** Genes previously reported to be disease-associated in both WTCCC paper and HuGE Navigator database

Piriyapongsa et al. BMC Genomics 2012 13(Suppl 7):S2   doi:10.1186/1471-2164-13-S7-S2

Open Data