Table 3 Twelve SNPs with median FLCN expression values in Lung and Skin (exposed) from GTex, and their alternate allele frequencies
From: Genetic insight into Birt–Hogg–Dubé syndrome in Indian patients reveals novel mutations at FLCN
Sl. No. SNPs | COORD | SNP ID | Annotation | Ref allele | Alt allele frequency (South Asian/Asian) | Lung (median values of gene expression) | Skin-exposed (median values of gene expression) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
REF | HET | ALT | p-value | REF | HET | ALT | p-value | ||||||
SNP 1 | 17,236,986 | rs41345949 | 5′ UTR | C | T = 0.03/0.05 | − 0.06 (440) | 0.27 (69) | N.A | 1.10E−07 | – | – | – | – |
SNP 2 | 17,212,319 | rs7218992 | 3′ UTR | C | A = –/0.06 | 0.126 (384) | − 0.37 (119) | − 0.91 (12) | 8.90E−14 | 0.05 (456) | − 0.22 (137) | − 0.500 (12) | 4.30E−07 |
SNP 3 | 17,213,262 | rs12602675 | 3′ UTR | C | T = 0.08/0.08 | 0.014 (478) | − 0.29 (37) | N.A | 0.00011 | 0.02 (564) | − 0.52 (40) | N.A | 1.10E−09 |
SNP 4 | 17,221,501 | rs3744124 | Intronic | C | T = 0.11/0.12 | 0.07 (452) | − 0.44 (62) | N.A | 2.40E−09 | 0.06 (529) | − 0.44 (76) | N.A | 3.40E−18 |
SNP 5 | 17,226,931 | rs6502565 | Intronic | C | T = 0.12/0.13 | 0.068 (451) | − 0.44 (62) | N.A | 1.80E−09 | 0.06 (528) | − 0.46 (76) | N.A | 1.30E−17 |
SNP 6 | 17,226,956 | rs76319098 | Intronic | C | T = 0.12/0.13 | 0.05 (466) | − 0.47 (47) | N.A | 1.80E−09 | 0.05 (548) | − 0.55 (56) | N.A | 1.20E−17 |
SNP 7 | 17,228,852 | rs79717038 | Intronic | G | A = 0.12/0.13 | 0.06 (464) | − 0.47 (49) | N.A | 2.70E−08 | 0.06 (543) | − 0.58 (61) | N.A | 3.10E−19 |
SNP 8 | 17,214,314 | rs8067893 | Intronic | G | A = –/0.11 | 0.134 (340) | − 0.255 (151) | − 0.52 (24) | 2.80E−12 | 0.08 (407) | − 0.23 (168) | 0.03 (30) | 1.70E−07 |
SNP 9 | 17,220,853 | rs41323249 | Intronic | C | T = 0.09/0.11 | 0.14 (359) | − 0.34 (139) | − 0.50 (17) | 2.60E−14 | 0.07 (430) | − 0.12 (153) | − 0.73 (22) | 4.40E− 08 |