Variant report

Variant	rs12671822
Chromosome Location	chr7:150421600-150421601
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11973417	0.88[EUR][1000 genomes]
rs11983348	0.88[EUR][1000 genomes]
rs11983413	0.88[EUR][1000 genomes]
rs2058448	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2058449	1.00[JPT][hapmap]
rs2080052	0.95[EUR][1000 genomes]
rs2098221	0.95[EUR][1000 genomes]
rs28736331	0.91[EUR][1000 genomes]
rs3807383	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4725355	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4725358	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4725359	0.85[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs58288826	0.88[EUR][1000 genomes]
rs59274837	0.88[EUR][1000 genomes]
rs59953726	0.83[ASN][1000 genomes]
rs60774275	0.88[EUR][1000 genomes]
rs60958118	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61199880	0.93[EUR][1000 genomes]
rs6955828	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6960420	0.83[ASN][1000 genomes]
rs6960820	0.93[EUR][1000 genomes]
rs6972456	1.00[JPT][hapmap]
rs73474878	0.88[EUR][1000 genomes]
rs73474880	0.88[EUR][1000 genomes]
rs73476552	0.91[EUR][1000 genomes]
rs73476554	0.93[EUR][1000 genomes]
rs73476564	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12671822	GIMAP5	cis	cerebellum	SCAN
rs12671822	GIMAP6	Cis_1M	lymphoblastoid	RTeQTL
rs12671822	ABCB8	cis	cerebellum	SCAN
rs12671822	GIMAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150414600-150421800	Weak transcription	Fetal Intestine Small	intestine
2	chr7:150415200-150424800	Weak transcription	Pancreas	Pancrea
3	chr7:150416800-150422000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:150417400-150423400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:150417800-150422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:150417800-150423400	Weak transcription	Thymus	Thymus
7	chr7:150418000-150424800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:150419800-150421600	Weak transcription	Gastric	stomach
9	chr7:150419800-150423400	Weak transcription	Right Ventricle	heart
10	chr7:150419800-150424400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr7:150420000-150422000	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr7:150420000-150422000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr7:150420000-150422600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr7:150420000-150423200	Weak transcription	Lung	lung
15	chr7:150420000-150423400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:150420000-150423400	Weak transcription	Fetal Thymus	thymus
17	chr7:150420200-150422600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:150420200-150423200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:150420400-150421800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr7:150420400-150422000	Weak transcription	HUVEC	blood vessel
21	chr7:150420600-150421800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:150420600-150423400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:150420600-150423400	Weak transcription	Dnd41	blood
24	chr7:150420800-150421600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:150420800-150422000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:150420800-150422000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr7:150420800-150422000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:150420800-150422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:150420800-150423200	Weak transcription	Adipose Nuclei	Adipose
30	chr7:150421000-150421800	Genic enhancers	Primary T cells from cord blood	blood
31	chr7:150421200-150421800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:150421400-150421800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr7:150421400-150422200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr7:150421400-150422800	Weak transcription	Liver	Liver
35	chr7:150421600-150421800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--

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