Variant report

Variant	rs6753830
Chromosome Location	chr2:20329353-20329354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20328337..20331162-chr2:20332733..20334257,2	K562	blood:
2	chr2:20329007..20330696-chr2:20423815..20426029,2	MCF-7	breast:
3	chr2:20329032..20331915-chr2:20335666..20338081,2	K562	blood:
4	chr2:20329242..20332304-chr2:20334345..20337488,3	MCF-7	breast:
5	chr2:20324363..20326500-chr2:20327352..20329382,2	MCF-7	breast:
6	chr2:20320341..20322786-chr2:20329123..20332598,3	MCF-7	breast:
7	chr2:20320788..20324422-chr2:20327103..20331085,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13019898	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs13023666	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17697743	0.83[TSI][hapmap]
rs6744463	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];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875412	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs973128	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs975951	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20323000-20329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20325800-20330800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20326200-20330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:20326400-20330600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:20326400-20334800	Weak transcription	Esophagus	oesophagus
6	chr2:20326400-20336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:20326600-20329800	Weak transcription	Small Intestine	intestine
8	chr2:20326600-20330600	Weak transcription	NHEK	skin
9	chr2:20326800-20330400	Weak transcription	Right Atrium	heart
10	chr2:20327600-20332000	Enhancers	Fetal Intestine Small	intestine
11	chr2:20328000-20332200	Enhancers	Fetal Intestine Large	intestine
12	chr2:20328200-20329800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr2:20328200-20331600	Enhancers	Colonic Mucosa	Colon
14	chr2:20328600-20331800	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:20328800-20329400	Enhancers	GM12878-XiMat	blood
16	chr2:20328800-20331000	Enhancers	Stomach Mucosa	stomach
17	chr2:20329000-20329600	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr2:20329000-20330000	Enhancers	Gastric	stomach
19	chr2:20329000-20331200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:20329200-20329600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:20329200-20329800	Enhancers	Liver	Liver
22	chr2:20329200-20330400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr2:20329200-20331000	Enhancers	Pancreas	Pancrea
24	chr2:20329200-20331200	Enhancers	Placenta	Placenta

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