Variant report

Variant	rs6531213
Chromosome Location	chr2:20344011-20344012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
2	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
3	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
4	chr2:20343488..20346809-chr2:20347899..20350701,3	MCF-7	breast:
5	chr2:20313693..20315548-chr2:20343549..20346217,2	MCF-7	breast:
6	chr2:20343897..20346310-chr2:20367652..20370210,2	MCF-7	breast:
7	chr2:20343375..20346267-chr2:20420870..20424774,4	MCF-7	breast:
8	chr2:20338664..20345614-chr2:20377409..20381353,9	MCF-7	breast:
9	chr2:20341298..20344262-chr2:20354699..20358501,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction
ENSG00000213729	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10196396	0.81[JPT][hapmap]
rs1398949	0.81[CEU][hapmap]
rs1398950	0.92[CEU][hapmap]
rs17697993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666294	0.81[JPT][hapmap]
rs4666295	0.81[JPT][hapmap]
rs6725416	0.80[JPT][hapmap]
rs981395	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs981396	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20334200-20346600	Enhancers	Placenta	Placenta
3	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:20338000-20346800	Enhancers	HMEC	breast
6	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
7	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:20340000-20345200	Weak transcription	Fetal Lung	lung
9	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:20341000-20344800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:20341200-20344800	Weak transcription	Colonic Mucosa	Colon
15	chr2:20341200-20345200	Weak transcription	Left Ventricle	heart
16	chr2:20341400-20344800	Weak transcription	Spleen	Spleen
17	chr2:20341400-20345000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:20341400-20345200	Weak transcription	HSMMtube	muscle
19	chr2:20341400-20345400	Weak transcription	Right Ventricle	heart
20	chr2:20341400-20345600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:20341600-20345200	Weak transcription	K562	blood
22	chr2:20341600-20345600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:20341800-20345000	Weak transcription	Liver	Liver
24	chr2:20341800-20348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:20341800-20348600	Weak transcription	Adipose Nuclei	Adipose
26	chr2:20341800-20348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:20342000-20344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:20342000-20344600	Weak transcription	HUVEC	blood vessel
29	chr2:20342000-20346200	Weak transcription	Osteobl	bone
30	chr2:20342000-20346400	Weak transcription	NHDF-Ad	bronchial
31	chr2:20342000-20348000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:20342000-20348200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:20342000-20348400	Weak transcription	NHLF	lung
34	chr2:20342000-20348600	Weak transcription	Hela-S3	cervix
35	chr2:20342800-20347000	Enhancers	Stomach Mucosa	stomach
36	chr2:20343000-20345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:20343000-20346400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:20343200-20345400	Weak transcription	Fetal Intestine Small	intestine
39	chr2:20343400-20344800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:20343400-20345200	Weak transcription	NHEK	skin
41	chr2:20343400-20345400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:20343400-20345600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:20343400-20346200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:20343400-20348400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:20343600-20346000	Enhancers	Esophagus	oesophagus
46	chr2:20343800-20344600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:20344000-20344200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:20344000-20345200	Weak transcription	A549	lung
49	chr2:20344000-20348200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links