Variant report

Variant	rs12540475
Chromosome Location	chr7:106886295-106886296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1002935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1018946	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1018947	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10253172	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs10253291	0.84[CEU][hapmap]
rs10487271	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953529	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953530	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953531	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953533	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953534	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953535	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953537	0.93[ASN][1000 genomes]
rs1121312	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761181	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11762152	0.82[ASN][1000 genomes]
rs11764448	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766060	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11767623	0.80[AMR][1000 genomes]
rs11769527	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769861	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11769901	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773514	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12154285	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12155231	0.80[EUR][1000 genomes]
rs12531187	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532447	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532849	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532953	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532967	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533516	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533767	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534000	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534676	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12535081	0.82[EUR][1000 genomes]
rs12535258	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12535814	0.92[ASN][1000 genomes]
rs12536485	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12536491	0.97[ASN][1000 genomes]
rs12536574	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12536603	0.95[ASN][1000 genomes]
rs12537011	0.93[ASN][1000 genomes]
rs12537374	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537730	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537733	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12538090	0.82[EUR][1000 genomes]
rs12538769	0.83[EUR][1000 genomes]
rs12538848	0.83[EUR][1000 genomes]
rs12705405	0.80[AMR][1000 genomes]
rs1548523	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548524	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17349904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17350182	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17427123	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17427158	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17427849	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17428071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17428126	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17428504	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17429118	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17429146	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981696	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs1989814	0.92[ASN][1000 genomes]
rs2023892	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2107318	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2107319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2189501	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249043	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299422	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395859	0.93[ASN][1000 genomes]
rs257371	0.80[AMR][1000 genomes]
rs257372	0.80[AMR][1000 genomes]
rs257373	0.80[AMR][1000 genomes]
rs257375	0.80[AMR][1000 genomes]
rs257377	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs257378	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs257381	0.80[AMR][1000 genomes]
rs257382	0.80[AMR][1000 genomes]
rs257385	0.82[AMR][1000 genomes]
rs257386	0.82[AMR][1000 genomes]
rs257387	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs2894459	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3729876	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs3729877	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs3757713	0.92[ASN][1000 genomes]
rs3779498	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779500	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs3801958	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801959	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3801963	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801965	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815148	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823959	0.93[ASN][1000 genomes]
rs3823960	0.93[ASN][1000 genomes]
rs4727670	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4727671	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730222	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4730223	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4730224	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4730226	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730227	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730228	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730229	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730231	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730232	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730233	0.83[EUR][1000 genomes]
rs57525841	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58319984	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58663672	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59900773	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60255281	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61014091	0.82[ASN][1000 genomes]
rs61406169	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61511581	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61673847	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466160	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs6466162	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6946036	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946931	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs6947675	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6947857	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs6949961	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951639	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6960148	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs6960813	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963917	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6964798	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6964966	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965001	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967638	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6967639	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967745	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6971675	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6971774	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6977868	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs7777976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7779062	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781947	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7783181	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783562	0.95[ASN][1000 genomes]
rs7789500	0.89[ASN][1000 genomes]
rs7789678	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7793594	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794598	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7794915	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7794965	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7798223	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800443	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803290	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807648	0.84[EUR][1000 genomes]
rs7981	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9641378	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997311	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2756226	chr7:106850755-106944563	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv1016691	chr7:106880953-106960515	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540475	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106844600-106888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:106846000-106925800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:106850400-106890000	Weak transcription	Hela-S3	cervix
4	chr7:106850800-106895200	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:106851000-106897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:106851000-106946000	Weak transcription	Esophagus	oesophagus
7	chr7:106851200-106888200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:106851200-106892400	Weak transcription	Gastric	stomach
9	chr7:106851200-106892600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:106853400-106925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:106863800-106887400	Weak transcription	Thymus	Thymus
12	chr7:106864000-106889600	Weak transcription	Spleen	Spleen
13	chr7:106865000-106887000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:106865600-106888200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:106865600-106890600	Weak transcription	Aorta	Aorta
16	chr7:106865600-106892400	Weak transcription	HepG2	liver
17	chr7:106866600-106909600	Weak transcription	Placenta	Placenta
18	chr7:106867000-106888000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:106867800-106889800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:106870800-106887600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:106871600-106889800	Weak transcription	NHDF-Ad	bronchial
22	chr7:106872000-106889800	Weak transcription	Fetal Lung	lung
23	chr7:106874000-106888200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:106874000-106888200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:106874000-106890200	Weak transcription	GM12878-XiMat	blood
26	chr7:106874000-106917800	Weak transcription	Osteobl	bone
27	chr7:106874000-106922600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:106874000-106929200	Weak transcription	NH-A	brain
29	chr7:106874000-106945600	Weak transcription	Pancreas	Pancrea
30	chr7:106874800-106886400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:106875000-106888200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:106875000-106889200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:106875000-106890600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:106875400-106887000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:106875400-106908000	Weak transcription	HMEC	breast
36	chr7:106875600-106898400	Weak transcription	HUVEC	blood vessel
37	chr7:106876600-106890000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:106877200-106886400	Weak transcription	Fetal Intestine Large	intestine
39	chr7:106877600-106887200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:106877800-106888000	Weak transcription	HSMM	muscle
41	chr7:106878200-106888200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:106878800-106886400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:106878800-106895000	Weak transcription	K562	blood
44	chr7:106879000-106887000	Weak transcription	Ovary	ovary
45	chr7:106879600-106887000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:106881200-106895600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:106882400-106890000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:106882600-106889200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr7:106883000-106918800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr7:106883200-106887000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links