Variant report

Variant	rs7017776
Chromosome Location	chr8:19362768-19362769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10088454	0.87[CHD][hapmap]
rs10089231	0.87[CHD][hapmap]
rs10101192	0.87[CHD][hapmap]
rs10105097	0.80[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10105363	0.83[CHD][hapmap]
rs10109274	0.87[CHD][hapmap]
rs1013438	0.87[CEU][hapmap]
rs10503653	0.83[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10888165	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11204044	0.80[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11204046	0.87[CEU][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204047	0.94[CEU][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204048	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204049	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204050	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11204052	0.88[ASN][1000 genomes]
rs11777566	0.84[ASN][1000 genomes]
rs11778734	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11780475	0.84[ASN][1000 genomes]
rs11783263	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12682196	0.89[JPT][hapmap]
rs13250181	0.89[JPT][hapmap]
rs13261442	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13261732	0.89[JPT][hapmap]
rs13265751	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13266857	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13267265	0.92[ASN][1000 genomes]
rs13267569	0.92[ASN][1000 genomes]
rs13276417	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13280711	0.86[ASN][1000 genomes]
rs13282951	0.87[CHD][hapmap]
rs17128525	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17128556	0.87[CHD][hapmap]
rs17128604	0.83[CHD][hapmap]
rs17479777	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490401	0.83[CHD][hapmap]
rs28671342	0.85[ASN][1000 genomes]
rs2958576	0.87[CEU][hapmap]
rs3185	0.89[JPT][hapmap]
rs3923920	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4073790	0.86[ASN][1000 genomes]
rs4073791	0.86[ASN][1000 genomes]
rs4244451	0.83[ASN][1000 genomes]
rs4244452	0.84[ASN][1000 genomes]
rs4244453	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4244454	0.81[CEU][hapmap]
rs4273861	0.83[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap]
rs4311666	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4317590	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4319111	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339658	0.84[ASN][1000 genomes]
rs4410924	0.87[CEU][hapmap]
rs4413788	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4442163	0.93[ASN][1000 genomes]
rs4455848	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4472532	0.87[CHD][hapmap]
rs4483172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4484715	0.80[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4513991	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4524812	0.84[ASN][1000 genomes]
rs4554481	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4599829	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4614013	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4631482	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631483	0.88[ASN][1000 genomes]
rs4921646	0.84[ASN][1000 genomes]
rs4921647	0.83[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4921648	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921649	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921651	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4921652	0.92[ASN][1000 genomes]
rs4921653	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4921654	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4921655	0.88[ASN][1000 genomes]
rs4921656	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4921657	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922034	0.83[ASN][1000 genomes]
rs4922036	0.89[JPT][hapmap]
rs4922037	0.91[ASN][1000 genomes]
rs4922038	0.93[ASN][1000 genomes]
rs4922039	0.93[ASN][1000 genomes]
rs4922041	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4922044	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922045	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922047	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922048	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4922049	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922065	0.87[CEU][hapmap]
rs5013219	0.84[ASN][1000 genomes]
rs6586836	0.83[ASN][1000 genomes]
rs6586837	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6586838	0.83[ASN][1000 genomes]
rs6586839	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6586840	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6586842	0.87[TSI][hapmap]
rs6586843	0.87[CEU][hapmap]
rs6984449	0.89[JPT][hapmap]
rs6984644	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6988743	0.86[ASN][1000 genomes]
rs6991941	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6994352	0.88[ASW][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs6998334	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998991	0.96[ASN][1000 genomes]
rs6999542	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7002643	0.83[CHD][hapmap]
rs7005075	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs73585587	0.80[ASN][1000 genomes]
rs7460541	0.93[ASN][1000 genomes]
rs7464357	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7464358	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7814548	0.87[CHD][hapmap]
rs7816777	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7818691	0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7828197	0.89[ASN][1000 genomes]
rs7830404	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7838412	0.87[CEU][hapmap]
rs7839041	0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7841402	0.81[CEU][hapmap]
rs9644628	0.86[ASN][1000 genomes]
rs9644629	0.86[ASN][1000 genomes]
rs9644630	0.84[ASN][1000 genomes]
rs9644631	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
6	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv890624	chr8:19319061-19456270	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7017776	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
2	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
3	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:19348200-19364000	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:19348200-19367400	Weak transcription	Fetal Brain Female	brain
6	chr8:19350200-19362800	Weak transcription	Gastric	stomach
7	chr8:19351200-19369000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr8:19353400-19367600	Weak transcription	Brain Anterior Caudate	brain
9	chr8:19353400-19367600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:19354400-19367800	Weak transcription	Brain Substantia Nigra	brain
11	chr8:19354800-19366000	Weak transcription	Brain Angular Gyrus	brain
12	chr8:19355200-19363200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr8:19355800-19367600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:19356000-19368400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:19356400-19368600	Weak transcription	Thymus	Thymus
16	chr8:19357800-19362800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr8:19358000-19365000	Strong transcription	Primary B cells from cord blood	blood
18	chr8:19358200-19363000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr8:19358200-19364200	Weak transcription	Hela-S3	cervix
20	chr8:19358400-19363800	Weak transcription	Osteobl	bone
21	chr8:19359000-19364200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr8:19359400-19363400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:19359800-19367800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr8:19360000-19362800	Weak transcription	Right Atrium	heart
25	chr8:19360800-19363800	Weak transcription	Brain Germinal Matrix	brain
26	chr8:19360800-19364800	Strong transcription	A549	lung
27	chr8:19361000-19362800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr8:19361000-19365600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:19361400-19363000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr8:19361400-19363800	Transcr. at gene 5' and 3'	Placenta	Placenta
31	chr8:19361400-19364000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:19361600-19363800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr8:19362000-19363000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr8:19362000-19363200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr8:19362000-19363200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr8:19362000-19364400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr8:19362000-19364400	Enhancers	NHDF-Ad	bronchial
38	chr8:19362000-19364600	Enhancers	Fetal Lung	lung
39	chr8:19362200-19362800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr8:19362200-19363000	Genic enhancers	Primary T cells from cord blood	blood
41	chr8:19362200-19363000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr8:19362200-19363200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr8:19362200-19363400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr8:19362200-19363800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr8:19362200-19364200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr8:19362400-19363400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:19362400-19363600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr8:19362600-19362800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:19362600-19362800	Enhancers	Fetal Thymus	thymus
50	chr8:19362600-19362800	Enhancers	Small Intestine	intestine

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