Variant report

Variant	rs7180675
Chromosome Location	chr15:39939566-39939567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39934745..39936337-chr15:39938200..39940638,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10152640	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10520138	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10520142	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070226	0.89[ASN][1000 genomes]
rs11070227	0.89[ASN][1000 genomes]
rs11070228	0.89[ASN][1000 genomes]
rs11630406	0.91[ASN][1000 genomes]
rs11632117	0.92[ASN][1000 genomes]
rs11632879	0.89[ASN][1000 genomes]
rs11635103	0.91[ASN][1000 genomes]
rs11636823	0.92[ASN][1000 genomes]
rs11638041	0.89[ASN][1000 genomes]
rs11638558	0.89[ASN][1000 genomes]
rs11852591	0.89[ASN][1000 genomes]
rs11852649	0.89[ASN][1000 genomes]
rs11855487	0.89[ASN][1000 genomes]
rs11856971	0.89[ASN][1000 genomes]
rs12443011	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16969395	0.81[ASN][1000 genomes]
rs16969426	0.89[ASN][1000 genomes]
rs16969429	0.89[ASN][1000 genomes]
rs16969451	0.89[ASN][1000 genomes]
rs16969459	0.89[ASN][1000 genomes]
rs16969475	0.91[ASN][1000 genomes]
rs16969478	0.91[ASN][1000 genomes]
rs1876852	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1876853	0.89[ASN][1000 genomes]
rs2411300	0.86[EUR][1000 genomes]
rs2411310	0.88[AFR][1000 genomes]
rs2411313	0.92[ASN][1000 genomes]
rs2411314	0.90[ASN][1000 genomes]
rs2411315	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2412412	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2412413	0.89[ASN][1000 genomes]
rs2412414	0.89[ASN][1000 genomes]
rs2412415	0.88[ASN][1000 genomes]
rs2412416	0.89[ASN][1000 genomes]
rs2412417	0.89[ASN][1000 genomes]
rs2412418	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2898686	0.91[ASN][1000 genomes]
rs2898688	0.89[ASN][1000 genomes]
rs2898962	0.89[ASN][1000 genomes]
rs4319738	0.91[AFR][1000 genomes]
rs4319740	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4349120	0.89[ASN][1000 genomes]
rs4479205	0.89[ASN][1000 genomes]
rs4493017	0.90[AFR][1000 genomes]
rs4526992	0.92[ASN][1000 genomes]
rs4547308	0.89[ASN][1000 genomes]
rs4583211	0.93[ASN][1000 genomes]
rs4628934	0.89[ASN][1000 genomes]
rs59449051	0.93[ASN][1000 genomes]
rs60164392	0.89[ASN][1000 genomes]
rs60195210	0.89[ASN][1000 genomes]
rs61130460	0.91[ASN][1000 genomes]
rs61439563	0.92[ASN][1000 genomes]
rs61568256	0.91[ASN][1000 genomes]
rs66781090	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7162070	0.89[ASN][1000 genomes]
rs7162781	0.92[ASN][1000 genomes]
rs7167184	0.89[ASN][1000 genomes]
rs7168755	0.90[ASN][1000 genomes]
rs7170335	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176721	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179293	0.80[AMR][1000 genomes]
rs7179608	0.92[ASN][1000 genomes]
rs72725079	0.89[ASN][1000 genomes]
rs72725080	0.89[ASN][1000 genomes]
rs72725084	0.89[ASN][1000 genomes]
rs72725093	0.92[ASN][1000 genomes]
rs72725101	0.92[ASN][1000 genomes]
rs768663	0.82[EUR][1000 genomes]
rs8026916	0.89[ASN][1000 genomes]
rs8029602	0.91[ASN][1000 genomes]
rs8032289	0.89[ASN][1000 genomes]
rs8034594	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8039035	0.80[AMR][1000 genomes]
rs884584	0.92[ASN][1000 genomes]
rs9806365	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs999393	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39923800-39939600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:39937000-39941200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:39937800-39943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:39938000-39944400	Weak transcription	HSMMtube	muscle
5	chr15:39938000-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:39938200-39950800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:39938400-39941800	Weak transcription	Left Ventricle	heart

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