Variant report

Variant	rs389397
Chromosome Location	chr6:24964870-24964871
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11961358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332964	0.95[ASN][1000 genomes]
rs12332965	0.95[ASN][1000 genomes]
rs127485	0.91[ASN][1000 genomes]
rs1739305	1.00[ASN][1000 genomes]
rs1739326	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831597	0.95[ASN][1000 genomes]
rs1888931	0.95[ASN][1000 genomes]
rs364555	1.00[ASN][1000 genomes]
rs365630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366851	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs371051	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371847	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379970	1.00[ASN][1000 genomes]
rs381441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384245	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384476	0.87[ASN][1000 genomes]
rs385067	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385891	1.00[ASN][1000 genomes]
rs387070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389399	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs390218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390465	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs391652	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391937	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392899	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393228	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395417	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs396599	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400010	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs402518	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408655	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413194	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs418145	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs419479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420634	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426423	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438015	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403258	0.95[ASN][1000 genomes]
rs442135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449796	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450392	0.86[YRI][hapmap]
rs454251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555250	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569553	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57868523	0.95[ASN][1000 genomes]
rs581980	1.00[ASN][1000 genomes]
rs582056	1.00[ASN][1000 genomes]
rs584439	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs592258	1.00[ASN][1000 genomes]
rs607603	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs618388	0.91[ASN][1000 genomes]
rs622893	0.87[ASN][1000 genomes]
rs636915	1.00[ASN][1000 genomes]
rs651469	1.00[ASN][1000 genomes]
rs652324	1.00[ASN][1000 genomes]
rs660776	1.00[ASN][1000 genomes]
rs662629	1.00[ASN][1000 genomes]
rs673285	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6907762	0.90[ASN][1000 genomes]
rs6907920	0.95[ASN][1000 genomes]
rs6908148	0.95[ASN][1000 genomes]
rs6910136	0.95[ASN][1000 genomes]
rs6913176	0.90[ASN][1000 genomes]
rs6924615	0.95[ASN][1000 genomes]
rs6938547	0.95[ASN][1000 genomes]
rs6938772	0.90[ASN][1000 genomes]
rs73382387	0.95[ASN][1000 genomes]
rs73729556	0.90[ASN][1000 genomes]
rs73729573	0.95[ASN][1000 genomes]
rs7765763	0.95[ASN][1000 genomes]
rs9461085	0.95[ASN][1000 genomes]
rs9461087	0.95[ASN][1000 genomes]
rs9461088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9467363	0.90[ASN][1000 genomes]
rs9467364	0.90[ASN][1000 genomes]
rs9467368	0.95[ASN][1000 genomes]
rs9467369	0.95[ASN][1000 genomes]
rs9467370	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24952800-24966600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr6:24952800-24973200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:24954400-24980800	Weak transcription	Thymus	Thymus
5	chr6:24959400-24965000	Enhancers	Primary T cells from cord blood	blood
6	chr6:24960000-24966600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:24961800-24965000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:24961800-24965800	Weak transcription	Brain Germinal Matrix	brain
9	chr6:24961800-24966200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:24961800-24970400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:24961800-24971600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:24962400-24966600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:24962400-24969400	Weak transcription	Spleen	Spleen
14	chr6:24962600-24971200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:24962800-24966200	Weak transcription	Primary B cells from cord blood	blood
16	chr6:24963000-24968600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:24963000-24968800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:24963200-24967800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:24963400-24969200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:24964400-24966600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:24964600-24965000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:24964600-24965400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:24964600-24971400	Weak transcription	Gastric	stomach
24	chr6:24964800-24965800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:24964800-24967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links