Variant report

Variant	rs2817718
Chromosome Location	chr6:24894177-24894178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2747677	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2747683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817720	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2817722	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2817723	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2817724	0.89[ASN][1000 genomes]
rs2817725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817726	0.80[ASN][1000 genomes]
rs734014	1.00[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[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734015	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932494	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:24876000-24901800	Weak transcription	Spleen	Spleen
3	chr6:24878400-24899800	Weak transcription	Thymus	Thymus
4	chr6:24881200-24898400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr6:24881400-24895400	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr6:24882400-24904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:24882600-24899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:24884200-24899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:24885600-24896600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:24886600-24895000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr6:24887000-24900000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:24887400-24897400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:24887400-24898000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:24888200-24897400	Weak transcription	Fetal Brain Female	brain
16	chr6:24889000-24898600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:24889400-24899800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:24889600-24899600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:24889600-24900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:24890400-24896400	Genic enhancers	Primary T cells from cord blood	blood
21	chr6:24890600-24896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:24890600-24899200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
23	chr6:24890600-24900800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:24890800-24895400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:24891000-24902800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:24891400-24897000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:24891600-24897200	Weak transcription	NHDF-Ad	bronchial
28	chr6:24891600-24901400	Weak transcription	GM12878-XiMat	blood
29	chr6:24891600-24901800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:24891600-24908400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:24892000-24897200	Weak transcription	HSMMtube	muscle
32	chr6:24892000-24900200	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:24892600-24894800	Enhancers	Fetal Heart	heart
34	chr6:24892600-24895800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:24892600-24896600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:24892600-24898400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:24892800-24894600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:24892800-24897400	Strong transcription	Primary B cells from cord blood	blood
39	chr6:24893000-24897600	Weak transcription	Brain Germinal Matrix	brain
40	chr6:24893600-24894800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:24893800-24894800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:24893800-24896000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:24894000-24894800	Strong transcription	Fetal Thymus	thymus
44	chr6:24894000-24897400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links