Variant report

Variant	rs6531209
Chromosome Location	chr2:20334723-20334724
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20331753..20338544-chr2:20423396..20426851,7	MCF-7	breast:
2	chr2:20333229..20337003-chr2:20421997..20425401,4	MCF-7	breast:
3	chr2:20332851..20335555-chr2:20339124..20341592,3	K562	blood:
4	chr2:20322072..20326084-chr2:20334448..20336577,3	MCF-7	breast:
5	chr2:20334225..20337843-chr2:20372187..20375546,3	MCF-7	breast:
6	chr2:20333298..20335083-chr2:20336801..20339415,3	MCF-7	breast:
7	chr2:20332825..20334861-chr2:20412416..20414197,2	MCF-7	breast:
8	chr2:20329242..20332304-chr2:20334345..20337488,3	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11678155	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2090033	1.00[CHB][hapmap]
rs4666366	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4666368	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7563386	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs973129	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975950	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Amyotrophic lateral sclerosis (sporadic)	24529757	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20326400-20334800	Weak transcription	Esophagus	oesophagus
2	chr2:20326400-20336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:20331000-20335000	Weak transcription	Liver	Liver
4	chr2:20331000-20335600	Weak transcription	NHEK	skin
5	chr2:20331200-20334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20331200-20335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:20331200-20335400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:20331200-20335800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:20331400-20335600	Weak transcription	Fetal Lung	lung
10	chr2:20331600-20337000	Weak transcription	Colonic Mucosa	Colon
11	chr2:20331800-20335600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:20331800-20338600	Weak transcription	Small Intestine	intestine
13	chr2:20332000-20335600	Weak transcription	Fetal Intestine Small	intestine
14	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:20333000-20335600	Weak transcription	Fetal Kidney	kidney
16	chr2:20333600-20335400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:20334200-20334800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:20334200-20346600	Enhancers	Placenta	Placenta
19	chr2:20334400-20335600	Weak transcription	HMEC	breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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