Variant report

Variant	rs2462590
Chromosome Location	chr2:47284168-47284169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47283603..47286484-chr2:47288928..47291971,4	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11125114	1.00[CHB][hapmap]
rs13389149	0.85[CHB][hapmap]
rs13393256	1.00[CHB][hapmap]
rs1807327	1.00[CHB][hapmap]
rs1807328	1.00[CHB][hapmap]
rs2436772	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570511	0.82[EUR][1000 genomes]
rs2692216	1.00[CHB][hapmap]
rs2692219	1.00[CHB][hapmap]
rs2949785	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs940737	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs9973596	0.80[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:47270800-47296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:47272200-47292000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:47274200-47285200	Weak transcription	K562	blood
6	chr2:47274800-47292800	Weak transcription	Hela-S3	cervix
7	chr2:47276400-47284200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:47276600-47286200	Enhancers	Psoas Muscle	Psoas
9	chr2:47278600-47290800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:47279600-47284800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:47279800-47289000	Weak transcription	NHEK	skin
12	chr2:47280000-47285000	Weak transcription	Fetal Brain Female	brain
13	chr2:47280000-47287800	Weak transcription	HMEC	breast
14	chr2:47280400-47284800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:47281200-47284400	Genic enhancers	Spleen	Spleen
16	chr2:47281400-47286800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:47281600-47286600	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:47281600-47287600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:47282000-47293400	Enhancers	Brain Substantia Nigra	brain
20	chr2:47282200-47286800	Genic enhancers	NHLF	lung
21	chr2:47282200-47287000	Enhancers	Left Ventricle	heart
22	chr2:47282200-47288000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:47282400-47286000	Enhancers	Right Atrium	heart
24	chr2:47282400-47286200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:47282400-47286800	Genic enhancers	Fetal Stomach	stomach
26	chr2:47282400-47286800	Enhancers	HSMMtube	muscle
27	chr2:47282400-47288000	Enhancers	Brain Angular Gyrus	brain
28	chr2:47282400-47289800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:47282600-47284400	Genic enhancers	Esophagus	oesophagus
30	chr2:47282600-47285000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:47282600-47285200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr2:47282600-47285600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:47282600-47286000	Enhancers	Ovary	ovary
34	chr2:47282600-47286600	Enhancers	Lung	lung
35	chr2:47282600-47286600	Enhancers	NHDF-Ad	bronchial
36	chr2:47282600-47286800	Enhancers	Right Ventricle	heart
37	chr2:47282600-47287000	Enhancers	Adipose Nuclei	Adipose
38	chr2:47282600-47288000	Enhancers	Brain Hippocampus Middle	brain
39	chr2:47282800-47284600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr2:47282800-47284800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:47282800-47285000	Enhancers	Colon Smooth Muscle	Colon
42	chr2:47282800-47285200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:47282800-47285600	Enhancers	A549	lung
44	chr2:47282800-47285800	Enhancers	HSMM	muscle
45	chr2:47282800-47286000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:47282800-47286000	Enhancers	NH-A	brain
47	chr2:47282800-47286200	Enhancers	Fetal Lung	lung
48	chr2:47282800-47286400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:47282800-47286400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:47282800-47286600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links