Variant report

Variant	rs678784
Chromosome Location	chr6:24958507-24958508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11961358	1.00[JPT][hapmap]
rs127485	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1739305	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1739326	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1753528	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs364555	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs366851	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs379970	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs385891	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs387070	1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs389399	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs390218	1.00[JPT][hapmap]
rs390465	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs391652	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs391937	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs392661	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs393228	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs395417	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs396599	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs400010	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs408655	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs413194	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs418145	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs420634	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs432006	0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs438015	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs449796	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs451084	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs555250	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs569553	0.96[ASN][1000 genomes]
rs581980	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs582056	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs584439	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs592258	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs607603	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618388	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs622893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs636915	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs651469	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs652324	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs660776	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs662629	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs673285	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9461088	1.00[JPT][hapmap]

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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24951200-24960800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:24951800-24961600	Weak transcription	Spleen	Spleen
4	chr6:24952800-24964800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr6:24952800-24966600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:24952800-24973200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:24953200-24959000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:24954400-24980800	Weak transcription	Thymus	Thymus
9	chr6:24954600-24959600	Weak transcription	Fetal Thymus	thymus
10	chr6:24955200-24959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:24955200-24959200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:24957000-24958800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:24957200-24959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:24957200-24959400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:24957400-24959400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:24957400-24959400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:24957400-24959600	Weak transcription	Primary B cells from cord blood	blood
18	chr6:24957400-24959600	Weak transcription	GM12878-XiMat	blood
19	chr6:24957600-24958800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:24957600-24959000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:24957600-24959400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:24957600-24959800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:24957800-24958800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:24957800-24958800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:24957800-24959200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:24957800-24959400	Weak transcription	Primary T cells from cord blood	blood
27	chr6:24958200-24959400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:24958400-24958800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:24958400-24958800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:24958400-24959400	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links