Variant report

Variant	rs26894
Chromosome Location	chr5:80417663-80417664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12659839	0.81[JPT][hapmap]
rs153229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153230	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153231	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153232	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153233	0.90[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153234	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs153235	0.83[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs153236	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs153237	0.93[ASN][1000 genomes]
rs153238	0.93[ASN][1000 genomes]
rs153239	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs153240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153241	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153242	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153243	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153244	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168718	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17213885	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs173596	0.81[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs190339	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs193786	0.86[ASN][1000 genomes]
rs2454870	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248980	0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248981	0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248982	0.91[ASN][1000 genomes]
rs248983	0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248984	0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs248985	0.83[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs248986	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs248987	0.83[ASN][1000 genomes]
rs248988	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248989	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248992	0.90[JPT][hapmap]
rs26889	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26890	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26893	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26896	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26898	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27513	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27558	0.85[CEU][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27781	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28820	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs34115	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs34116	0.89[JPT][hapmap]
rs34117	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs34120	0.86[ASN][1000 genomes]
rs34121	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs34122	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs382926	0.81[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs40046	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs457365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs466044	0.96[ASN][1000 genomes]
rs58200570	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv882232	chr5:80393949-80436584	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80375000-80422600	Weak transcription	Left Ventricle	heart
2	chr5:80383400-80421600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:80401600-80421400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:80401800-80420200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:80401800-80420600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:80404800-80428200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:80406600-80417800	Strong transcription	Primary T cells from cord blood	blood
8	chr5:80407000-80428000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:80408400-80418400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr5:80408800-80426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:80409800-80422600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:80410200-80417800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:80410600-80419600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:80410600-80421600	Weak transcription	Brain Substantia Nigra	brain
15	chr5:80410600-80432400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:80410600-80446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:80411200-80427800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:80411800-80421800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:80413400-80424800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:80414000-80421200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:80414200-80438000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:80414600-80417800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:80415200-80421200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:80415400-80419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:80415600-80421600	Weak transcription	Ovary	ovary
26	chr5:80416000-80423400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:80416600-80418600	Enhancers	Fetal Brain Female	brain
28	chr5:80416600-80422800	Enhancers	Liver	Liver
29	chr5:80416800-80417800	Enhancers	Fetal Brain Male	brain
30	chr5:80416800-80418600	Enhancers	Fetal Lung	lung
31	chr5:80417000-80418200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:80417000-80418600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:80417000-80418800	Enhancers	Adipose Nuclei	Adipose
34	chr5:80417000-80419800	Enhancers	Brain Germinal Matrix	brain
35	chr5:80417200-80417800	Enhancers	Brain Hippocampus Middle	brain
36	chr5:80417400-80417800	Enhancers	Right Atrium	heart
37	chr5:80417400-80418200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr5:80417600-80417800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:80417600-80417800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:80417600-80417800	Enhancers	Brain Angular Gyrus	brain
41	chr5:80417600-80418000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:80417600-80418200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr5:80417600-80418200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:80417600-80418200	Enhancers	Brain Anterior Caudate	brain
45	chr5:80417600-80418800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:80417600-80419600	Weak transcription	Fetal Intestine Small	intestine
47	chr5:80417600-80419800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:80417600-80421200	Weak transcription	HepG2	liver

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