Variant report

Variant	rs11072793
Chromosome Location	chr15:79006442-79006443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072787	0.89[CEU][hapmap]
rs11072794	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072799	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629639	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11629824	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633170	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633519	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852887	0.83[EUR][1000 genomes]
rs11852909	0.86[EUR][1000 genomes]
rs11856441	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12899940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901228	0.84[EUR][1000 genomes]
rs12907178	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907511	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1383634	0.86[EUR][1000 genomes]
rs1383635	0.86[EUR][1000 genomes]
rs1809412	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1809414	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1814880	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1825086	0.86[EUR][1000 genomes]
rs1904920	0.82[EUR][1000 genomes]
rs2219939	0.86[EUR][1000 genomes]
rs4887074	0.84[CEU][hapmap]
rs4887078	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887085	0.80[ASN][1000 genomes]
rs4887091	0.94[CEU][hapmap]
rs6495317	0.84[ASN][1000 genomes]
rs6495318	0.85[ASN][1000 genomes]
rs7163236	0.83[ASN][1000 genomes]
rs7170552	0.85[ASN][1000 genomes]
rs7170563	0.82[ASN][1000 genomes]
rs7182567	0.95[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs72625802	0.85[ASN][1000 genomes]
rs8039600	0.84[ASN][1000 genomes]
rs8043123	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs899997	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9888691	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11072793	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs11072793	TMED3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79002200-79007400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:79005800-79008200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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