Variant report

Variant	rs11096639
Chromosome Location	chr2:20305429-20305430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20302794..20305910-chr2:20337863..20340597,3	MCF-7	breast:
2	chr2:20304028..20306367-chr2:20390369..20392912,2	MCF-7	breast:
3	chr2:20303170..20305756-chr2:20308003..20310603,2	MCF-7	breast:
4	chr2:20302713..20305705-chr2:20312784..20315987,4	MCF-7	breast:
5	chr2:20299695..20307724-chr2:20421846..20426859,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10169811	0.95[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10171384	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10195803	0.95[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10199614	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10207632	0.85[EUR][1000 genomes]
rs10208355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1028054	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1028055	0.95[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11677734	0.86[CEU][hapmap]
rs11679737	0.81[CEU][hapmap]
rs11685443	0.82[CEU][hapmap]
rs11685788	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11689490	0.91[CEU][hapmap]
rs11690530	0.86[CEU][hapmap]
rs11692546	0.86[CEU][hapmap]
rs11900576	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12998930	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13005386	0.86[CEU][hapmap]
rs13391566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34367401	0.83[EUR][1000 genomes]
rs34481015	0.84[EUR][1000 genomes]
rs55971461	0.86[EUR][1000 genomes]
rs6531203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6531204	0.91[CEU][hapmap]
rs6531205	0.91[CEU][hapmap]
rs6531206	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6531207	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs66598678	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708655	0.91[CEU][hapmap]
rs6709349	0.91[CEU][hapmap]
rs6719494	0.86[EUR][1000 genomes]
rs6749952	0.84[EUR][1000 genomes]
rs7556745	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs7558628	0.95[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs7561381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7572608	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7582437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7583420	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7609013	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs878983	0.85[CEU][hapmap]
rs907864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11096639	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20298400-20307800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:20301200-20306400	Weak transcription	HUVEC	blood vessel
3	chr2:20303400-20306400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:20303600-20307000	Enhancers	Esophagus	oesophagus
5	chr2:20304000-20306200	Weak transcription	HMEC	breast
6	chr2:20304200-20306000	Enhancers	Stomach Mucosa	stomach
7	chr2:20304600-20305800	Enhancers	Placenta	Placenta
8	chr2:20304600-20306800	Weak transcription	Fetal Lung	lung
9	chr2:20304800-20305600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:20304800-20306400	Weak transcription	Pancreas	Pancrea
11	chr2:20304800-20308600	Weak transcription	Liver	Liver
12	chr2:20305000-20306400	Weak transcription	Spleen	Spleen
13	chr2:20305200-20307200	Weak transcription	HepG2	liver
14	chr2:20305200-20308600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:20305400-20305600	Weak transcription	Gastric	stomach
16	chr2:20305400-20306400	Weak transcription	Lung	lung

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