Variant report

Variant	rs13266857
Chromosome Location	chr8:19364515-19364516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10105097	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10105464	0.82[ASN][1000 genomes]
rs10282938	0.80[CHD][hapmap]
rs10503653	0.89[JPT][hapmap]
rs10888165	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap]
rs11204046	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11204047	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11204048	0.86[ASN][1000 genomes]
rs11204049	0.88[ASN][1000 genomes]
rs11204050	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11204052	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778734	0.89[JPT][hapmap]
rs11780475	0.96[ASN][1000 genomes]
rs11783263	0.93[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs11786904	0.80[ASN][1000 genomes]
rs12682196	0.80[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13250181	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs13261442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13261732	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs13265751	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13267265	0.83[ASN][1000 genomes]
rs13267569	0.83[ASN][1000 genomes]
rs13267801	0.80[ASN][1000 genomes]
rs13275706	0.80[ASN][1000 genomes]
rs13276417	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13280711	0.99[ASN][1000 genomes]
rs17128525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479777	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28671342	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3185	0.80[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs3923920	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4073790	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073791	0.99[ASN][1000 genomes]
rs4244453	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4273861	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4311666	0.89[JPT][hapmap]
rs4317590	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4319111	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4339658	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4413788	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs4442163	0.81[ASN][1000 genomes]
rs4455848	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4483172	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4484715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4513991	0.88[ASN][1000 genomes]
rs4554481	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4599829	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4614013	0.85[ASN][1000 genomes]
rs4631482	0.86[ASN][1000 genomes]
rs4631483	0.92[CHB][hapmap];0.98[ASN][1000 genomes]
rs4921647	0.89[JPT][hapmap]
rs4921648	0.89[JPT][hapmap]
rs4921649	0.89[JPT][hapmap]
rs4921651	0.80[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4921652	0.83[ASN][1000 genomes]
rs4921653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4921654	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4921655	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4921656	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4921657	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4922035	0.80[ASN][1000 genomes]
rs4922036	0.80[CEU][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4922038	0.84[ASN][1000 genomes]
rs4922039	0.84[ASN][1000 genomes]
rs4922041	0.85[ASN][1000 genomes]
rs4922044	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4922045	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922046	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922047	0.80[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922048	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4922049	0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6586837	0.89[JPT][hapmap]
rs6586839	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984449	0.80[CEU][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6984644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986388	0.80[ASN][1000 genomes]
rs6988743	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6994352	0.89[JPT][hapmap]
rs6998334	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6998991	0.86[ASN][1000 genomes]
rs6999542	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7005075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006155	0.80[ASN][1000 genomes]
rs7017776	0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7460541	0.81[ASN][1000 genomes]
rs7464357	0.86[ASN][1000 genomes]
rs7464358	0.86[ASN][1000 genomes]
rs7816777	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs7818691	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7828197	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7830404	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7839041	0.89[JPT][hapmap]
rs9644628	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9644629	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9644630	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9644631	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]

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	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	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
4	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
5	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
6	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
7	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
8	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
9	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13266857	CSGALNACT1	cis	parietal	SCAN
rs13266857	CSGALNACT1	cis	cerebellum	SCAN
rs13266857	INTS10	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
2	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:19348200-19367400	Weak transcription	Fetal Brain Female	brain
4	chr8:19351200-19369000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr8:19353400-19367600	Weak transcription	Brain Anterior Caudate	brain
6	chr8:19353400-19367600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:19354400-19367800	Weak transcription	Brain Substantia Nigra	brain
8	chr8:19354800-19366000	Weak transcription	Brain Angular Gyrus	brain
9	chr8:19355800-19367600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:19356000-19368400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:19356400-19368600	Weak transcription	Thymus	Thymus
12	chr8:19358000-19365000	Strong transcription	Primary B cells from cord blood	blood
13	chr8:19359800-19367800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr8:19360800-19364800	Strong transcription	A549	lung
15	chr8:19361000-19365600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:19362000-19364600	Enhancers	Fetal Lung	lung
17	chr8:19362600-19364600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr8:19362600-19364600	Enhancers	Fetal Muscle Leg	muscle
19	chr8:19362800-19364800	Enhancers	Right Atrium	heart
20	chr8:19362800-19368400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr8:19363000-19365000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr8:19363000-19369600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:19363000-19372600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr8:19363200-19364600	Enhancers	Right Ventricle	heart
25	chr8:19363200-19365000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr8:19363200-19367800	Weak transcription	Colon Smooth Muscle	Colon
27	chr8:19363200-19368200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr8:19363200-19372800	Weak transcription	Spleen	Spleen
29	chr8:19363200-19376600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr8:19363400-19366000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr8:19363400-19367200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr8:19363400-19367400	Weak transcription	Aorta	Aorta
33	chr8:19363400-19368400	Enhancers	Primary T cells from cord blood	blood
34	chr8:19363400-19368400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr8:19363400-19368400	Weak transcription	Gastric	stomach
36	chr8:19363400-19368400	Weak transcription	Pancreas	Pancrea
37	chr8:19363600-19365600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr8:19363600-19367400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr8:19363800-19364600	Genic enhancers	Placenta	Placenta
40	chr8:19363800-19366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr8:19363800-19368400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr8:19364000-19364600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr8:19364000-19364600	Enhancers	Left Ventricle	heart
44	chr8:19364000-19365400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr8:19364200-19364800	Enhancers	Hela-S3	cervix
46	chr8:19364200-19365800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr8:19364200-19366600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr8:19364200-19367600	Weak transcription	Brain Hippocampus Middle	brain
49	chr8:19364200-19368400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr8:19364200-19368600	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links