Variant report

Variant	rs616582
Chromosome Location	chr2:111941995-111941996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111940752..111942733-chr2:111943898..111945698,2	K562	blood:
2	chr2:111941236..111945109-chr2:111946384..111948613,3	K562	blood:
3	chr2:111938737..111942201-chr2:111942427..111945208,3	K562	blood:
4	chr2:111939569..111942503-chr2:111952728..111955469,2	MCF-7	breast:
5	chr2:111941236..111945109-chr2:111946384..111948560,3	K562	blood:
6	chr2:111933860..111937323-chr2:111941659..111944364,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230499	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10166773	0.80[CHB][hapmap]
rs11123406	0.83[ASN][1000 genomes]
rs13396983	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs13398360	0.80[CHB][hapmap]
rs17558117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877331	0.85[CEU][hapmap]
rs1980045	0.81[CEU][hapmap];0.82[ASN][1000 genomes]
rs2015454	0.85[CEU][hapmap]
rs2241845	0.85[CEU][hapmap]
rs36018702	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3827536	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4849442	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs616130	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs6738028	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6746608	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs6750599	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs6753785	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758181	0.82[ASN][1000 genomes]
rs744531	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs7567444	0.85[CEU][hapmap]
rs9308731	0.85[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv520700	chr2:111931421-111948809	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111920800-111943000	Weak transcription	Right Ventricle	heart
2	chr2:111929400-111942200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:111933600-111945200	Enhancers	Fetal Intestine Small	intestine
4	chr2:111934000-111945000	Enhancers	Fetal Intestine Large	intestine
5	chr2:111936800-111942000	Weak transcription	Adipose Nuclei	Adipose
6	chr2:111936800-111942400	Weak transcription	Placenta	Placenta
7	chr2:111936800-111942400	Weak transcription	Gastric	stomach
8	chr2:111936800-111942400	Weak transcription	Left Ventricle	heart
9	chr2:111937600-111942400	Weak transcription	Liver	Liver
10	chr2:111937600-111942800	Weak transcription	Stomach Mucosa	stomach
11	chr2:111938400-111942800	Weak transcription	A549	lung
12	chr2:111939400-111944400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr2:111939400-111945400	Enhancers	Pancreas	Pancrea
14	chr2:111940000-111943200	Weak transcription	Right Atrium	heart
15	chr2:111940400-111943000	Weak transcription	K562	blood
16	chr2:111940600-111942600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr2:111940600-111942800	Weak transcription	HepG2	liver
18	chr2:111941600-111944400	Enhancers	Esophagus	oesophagus
19	chr2:111941800-111942400	Enhancers	Lung	lung
20	chr2:111941800-111943400	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links