Variant report

Variant	rs12465890
Chromosome Location	chr2:20085848-20085849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11680554	0.81[CEU][hapmap]
rs12464127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12466802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13005512	0.81[CEU][hapmap]
rs1370585	0.86[ASN][1000 genomes]
rs16987205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16987220	0.86[ASN][1000 genomes]
rs17695872	0.81[CEU][hapmap]
rs34400777	0.86[ASN][1000 genomes]
rs66496755	0.86[ASN][1000 genomes]
rs73214227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73214229	0.83[AMR][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20068800-20086200	Weak transcription	Spleen	Spleen
2	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
3	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
4	chr2:20069600-20087800	Weak transcription	Gastric	stomach
5	chr2:20069800-20097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20075400-20097600	Weak transcription	Fetal Kidney	kidney
7	chr2:20076400-20093600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:20076400-20097200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:20076600-20087000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr2:20076600-20097400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:20076600-20098200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:20076800-20086000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:20076800-20091000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:20076800-20095400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:20076800-20095800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:20076800-20097200	Weak transcription	Fetal Thymus	thymus
17	chr2:20076800-20098400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:20076800-20099800	Weak transcription	Fetal Intestine Large	intestine
19	chr2:20079200-20087000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:20079200-20098600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:20079400-20097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:20079800-20099000	Weak transcription	Thymus	Thymus
23	chr2:20081800-20095200	Weak transcription	Primary T cells from cord blood	blood
24	chr2:20082600-20087800	Weak transcription	Left Ventricle	heart
25	chr2:20083000-20086200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:20083000-20095400	Weak transcription	Fetal Brain Female	brain
27	chr2:20085600-20086600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:20085600-20086800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:20085600-20087000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:20085600-20088600	Weak transcription	Right Ventricle	heart
31	chr2:20085800-20086200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:20085800-20086600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:20085800-20086600	Enhancers	HSMMtube	muscle
34	chr2:20085800-20090000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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