Variant report

Variant	rs58188999
Chromosome Location	chr15:39906963-39906964
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	chr15:39894910..39896472-chr15:39906886..39909258,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10152903	1.00[ASN][1000 genomes]
rs10152951	1.00[ASN][1000 genomes]
rs1038097	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051442	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520141	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10520143	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10520146	0.84[EUR][1000 genomes]
rs12438058	1.00[ASN][1000 genomes]
rs12442155	1.00[ASN][1000 genomes]
rs12442221	1.00[ASN][1000 genomes]
rs1382443	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382444	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	1.00[ASN][1000 genomes]
rs16969487	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969491	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16969547	0.85[EUR][1000 genomes]
rs17631807	1.00[ASN][1000 genomes]
rs17632916	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17633107	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702987	1.00[ASN][1000 genomes]
rs17705806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706083	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17706179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813493	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988082	0.80[EUR][1000 genomes]
rs1988555	0.84[EUR][1000 genomes]
rs2228262	1.00[ASN][1000 genomes]
rs2228263	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411316	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2618156	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618160	0.91[EUR][1000 genomes]
rs2618161	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618164	0.91[EUR][1000 genomes]
rs2618165	0.91[EUR][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664123	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664136	0.90[EUR][1000 genomes]
rs2664137	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664138	0.90[EUR][1000 genomes]
rs2664140	0.91[EUR][1000 genomes]
rs2664142	0.91[EUR][1000 genomes]
rs28377784	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28549326	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28619289	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28622135	1.00[ASN][1000 genomes]
rs28653011	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34878675	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415979	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4503768	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45461294	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923835	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59578395	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59628570	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	1.00[ASN][1000 genomes]
rs62002378	1.00[ASN][1000 genomes]
rs62002379	1.00[ASN][1000 genomes]
rs62002380	1.00[ASN][1000 genomes]
rs62002384	1.00[ASN][1000 genomes]
rs6492905	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7179604	1.00[ASN][1000 genomes]
rs74008526	1.00[ASN][1000 genomes]
rs74008647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008648	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs880270	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs954152	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9972350	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	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:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39904000-39913400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:39905000-39908400	Weak transcription	HUVEC	blood vessel
3	chr15:39906200-39908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:39906400-39908400	Weak transcription	HMEC	breast
5	chr15:39906400-39908400	Weak transcription	NHEK	skin
6	chr15:39906600-39916000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:39906800-39908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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