Variant report

Variant	rs9644631
Chromosome Location	chr8:19370830-19370831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10105097	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10105464	0.83[ASN][1000 genomes]
rs10282938	0.84[CHD][hapmap]
rs10503653	0.89[JPT][hapmap]
rs10888165	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap]
rs11204046	0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11204047	0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11204048	0.90[ASN][1000 genomes]
rs11204049	0.89[ASN][1000 genomes]
rs11204050	0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11204052	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778734	0.89[JPT][hapmap]
rs11780475	0.97[ASN][1000 genomes]
rs11783263	0.93[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12682196	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs13250181	0.89[JPT][hapmap]
rs13261442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13261732	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13265751	0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13266857	0.80[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13267265	0.84[ASN][1000 genomes]
rs13267569	0.84[ASN][1000 genomes]
rs13276417	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13280711	0.97[ASN][1000 genomes]
rs17128525	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17479777	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28671342	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3185	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs3923920	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4073790	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073791	0.97[ASN][1000 genomes]
rs4244453	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4273861	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap]
rs4311666	0.89[JPT][hapmap]
rs4317590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4319111	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4339658	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4413788	0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4442163	0.83[ASN][1000 genomes]
rs4455848	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4483172	0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4484715	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4513991	0.89[ASN][1000 genomes]
rs4554481	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4599829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4614013	0.89[ASN][1000 genomes]
rs4631482	0.88[ASN][1000 genomes]
rs4631483	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs4921647	0.89[JPT][hapmap]
rs4921648	0.89[JPT][hapmap]
rs4921649	0.89[JPT][hapmap]
rs4921651	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921652	0.84[ASN][1000 genomes]
rs4921653	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4921654	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4921655	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4921656	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4921657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922036	0.89[JPT][hapmap]
rs4922037	0.80[ASN][1000 genomes]
rs4922038	0.85[ASN][1000 genomes]
rs4922039	0.85[ASN][1000 genomes]
rs4922041	0.89[ASN][1000 genomes]
rs4922044	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4922045	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4922046	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4922047	0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4922048	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922049	0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6586837	0.89[JPT][hapmap]
rs6586839	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6586840	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6984449	0.89[JPT][hapmap]
rs6984644	0.92[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6988743	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6994352	0.89[JPT][hapmap]
rs6998334	0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6998991	0.85[ASN][1000 genomes]
rs6999542	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7005075	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7017776	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7460541	0.83[ASN][1000 genomes]
rs7464357	0.88[ASN][1000 genomes]
rs7464358	0.88[ASN][1000 genomes]
rs7816777	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7818691	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7828197	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7830404	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7839041	0.89[JPT][hapmap]
rs9644628	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644629	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644630	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv610753	chr8:19364883-19439977	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1018057	chr8:19370830-19435399	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9644631	CSGALNACT1	cis	parietal	SCAN
rs9644631	CSGALNACT1	cis	cerebellum	SCAN
rs9644631	INTS10	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr8:19363000-19372600	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr8:19363200-19372800	Weak transcription	Spleen	Spleen
4	chr8:19363200-19376600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:19364800-19376400	Weak transcription	Hela-S3	cervix
6	chr8:19365400-19372400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr8:19365800-19372400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:19366600-19372400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr8:19367000-19385000	Weak transcription	Ovary	ovary
10	chr8:19368400-19371000	Enhancers	Left Ventricle	heart
11	chr8:19368400-19371200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:19368400-19372600	Enhancers	Primary B cells from peripheral blood	blood
13	chr8:19368600-19371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr8:19368800-19371400	Weak transcription	Thymus	Thymus
15	chr8:19368800-19372400	Enhancers	Primary T cells from cord blood	blood
16	chr8:19368800-19372600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr8:19368800-19372600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:19368800-19372600	Weak transcription	Placenta	Placenta
19	chr8:19368800-19372800	Weak transcription	Gastric	stomach
20	chr8:19369000-19372400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:19369000-19372600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr8:19369000-19372600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr8:19369200-19372400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr8:19369200-19373800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr8:19369600-19371400	Weak transcription	Fetal Thymus	thymus
26	chr8:19369600-19372400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:19369800-19372600	Enhancers	Primary B cells from cord blood	blood
28	chr8:19369800-19372800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:19370200-19372000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr8:19370600-19371600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:19370600-19372400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr8:19370600-19372400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr8:19370600-19372400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr8:19370600-19372600	Weak transcription	Lung	lung
35	chr8:19370600-19372600	Weak transcription	Pancreas	Pancrea
36	chr8:19370600-19372600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr8:19370800-19371600	Weak transcription	Brain Angular Gyrus	brain
38	chr8:19370800-19372600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:19370800-19372600	Weak transcription	Right Atrium	heart
40	chr8:19370800-19372600	Weak transcription	Right Ventricle	heart
41	chr8:19370800-19372800	Weak transcription	Brain Hippocampus Middle	brain
42	chr8:19370800-19374400	Weak transcription	A549	lung
43	chr8:19370800-19376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr8:19370800-19381200	Weak transcription	Fetal Stomach	stomach
45	chr8:19370800-19385000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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