Variant report

Variant	rs11072428
Chromosome Location	chr15:73942342-73942343
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73940424..73942779-chr15:73975265..73978457,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103855	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11072429	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072430	0.80[JPT][hapmap];0.87[MEX][hapmap]
rs11072431	0.80[JPT][hapmap]
rs11634399	0.82[AMR][1000 genomes]
rs12148532	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12148719	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12185108	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593246	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1383616	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1481088	0.83[ASN][1000 genomes]
rs1481089	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16958079	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743500	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4470111	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56413315	0.81[AMR][1000 genomes]
rs6495069	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495075	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs6495076	0.82[JPT][hapmap]
rs7169374	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176654	0.87[MEX][hapmap]
rs8023823	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028089	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8036954	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs8037836	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs899981	0.81[TSI][hapmap]
rs922687	0.84[ASN][1000 genomes]
rs9920359	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11072428	TLE3	cis	parietal	SCAN
rs11072428	NPTN	cis	parietal	SCAN
rs11072428	FEZ1	trans	lymphoblastoid	seeQTL
rs11072428	ARIH1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73935000-73942600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:73940600-73942600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:73940600-73942600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:73940800-73942600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:73940800-73942600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:73940800-73942600	Weak transcription	Hela-S3	cervix
7	chr15:73940800-73942800	Weak transcription	HMEC	breast
8	chr15:73940800-73943000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:73941000-73942400	Weak transcription	NHEK	skin
10	chr15:73941600-73944000	Enhancers	Primary monocytes fromperipheralblood	blood

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