Variant report

Variant	rs6744463
Chromosome Location	chr2:20334385-20334386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
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	chr2:20334225..20337843-chr2:20372187..20375546,3	MCF-7	breast:
5	chr2:20333298..20335083-chr2:20336801..20339415,3	MCF-7	breast:
6	chr2:20332825..20334861-chr2:20412416..20414197,2	MCF-7	breast:
7	chr2:20329242..20332304-chr2:20334345..20337488,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266059	Chromatin interaction
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13023666	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17697743	0.83[TSI][hapmap]
rs2348314	0.90[MEX][hapmap]
rs6531212	0.90[MEX][hapmap]
rs6753830	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs875411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875412	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs973128	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975951	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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

No data

Chromatin state (count:22 , 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	chr2:20334000-20334400	Enhancers	HMEC	breast
18	chr2:20334000-20334600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:20334000-20334600	Enhancers	Stomach Mucosa	stomach
20	chr2:20334200-20334400	Bivalent Enhancer	NH-A	brain
21	chr2:20334200-20334800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:20334200-20346600	Enhancers	Placenta	Placenta

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