Variant report

Variant	rs6747879
Chromosome Location	chr2:20074904-20074905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20074079..20076562-chr2:20079303..20081491,2	K562	blood:
2	chr2:20067006..20069123-chr2:20072397..20077057,4	K562	blood:
3	chr2:20073905..20076651-chr2:20094852..20097192,2	K562	blood:

Variant related genes	Relation type
ENSG00000228784	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10169726	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186182	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096625	0.90[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096626	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096627	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096628	0.96[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676372	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12615948	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617511	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1437865	0.93[YRI][hapmap]
rs2276605	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34354920	0.92[ASN][1000 genomes]
rs3731670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729518	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566500	0.83[JPT][hapmap]
rs7570541	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs7577847	0.86[EUR][1000 genomes]
rs7586775	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595902	0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs7595915	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608279	0.85[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs7608518	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306887	0.91[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:20068800-20086200	Weak transcription	Spleen	Spleen
3	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
4	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
5	chr2:20069200-20077600	Weak transcription	Fetal Lung	lung
6	chr2:20069400-20075600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:20069400-20075800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:20069400-20076000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:20069400-20076200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:20069400-20078600	Weak transcription	Placenta	Placenta
11	chr2:20069600-20076000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr2:20069600-20079000	Weak transcription	NHDF-Ad	bronchial
13	chr2:20069600-20079800	Weak transcription	Lung	lung
14	chr2:20069600-20087800	Weak transcription	Gastric	stomach
15	chr2:20069800-20075000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:20069800-20079200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:20070000-20075400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:20070000-20078000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:20070000-20081400	Weak transcription	Esophagus	oesophagus
21	chr2:20070200-20075400	Weak transcription	Fetal Thymus	thymus
22	chr2:20071000-20076000	Strong transcription	Fetal Intestine Small	intestine
23	chr2:20071400-20076800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:20071400-20076800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:20071400-20081800	Strong transcription	Primary T cells from cord blood	blood
26	chr2:20071800-20079200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:20072000-20076400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:20072200-20077000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:20072200-20084000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:20072600-20076600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:20072800-20076800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:20073000-20075800	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:20074000-20076800	Strong transcription	Fetal Intestine Large	intestine
34	chr2:20074200-20076800	Strong transcription	Primary B cells from cord blood	blood
35	chr2:20074400-20075400	Enhancers	Fetal Kidney	kidney
36	chr2:20074400-20078400	Strong transcription	Fetal Stomach	stomach
37	chr2:20074600-20075400	Weak transcription	Thymus	Thymus
38	chr2:20074600-20076000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:20074800-20077400	Weak transcription	Placenta Amnion	Placenta Amnion

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