Variant report

Variant	rs2618165
Chromosome Location	chr15:39862896-39862897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39858767..39865533-chr15:39870539..39876162,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap]
rs1038097	0.98[EUR][1000 genomes]
rs1051442	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10520145	1.00[JPT][hapmap]
rs10520146	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12324682	1.00[JPT][hapmap]
rs1382443	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1382444	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16969335	1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969487	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16969491	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs16969547	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17632916	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17633210	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17705806	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17706179	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1813493	0.98[EUR][1000 genomes]
rs1988082	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1988555	0.92[EUR][1000 genomes]
rs1994380	1.00[JPT][hapmap]
rs2129457	1.00[JPT][hapmap]
rs2228263	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2618156	0.98[EUR][1000 genomes]
rs2618160	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2618161	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2618163	0.82[YRI][hapmap]
rs2618164	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618167	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2664123	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2664136	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2664137	0.98[EUR][1000 genomes]
rs2664138	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs2664140	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2664142	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28377784	0.91[EUR][1000 genomes]
rs28549326	0.91[EUR][1000 genomes]
rs28619289	0.91[EUR][1000 genomes]
rs28653011	0.91[EUR][1000 genomes]
rs34878675	0.86[EUR][1000 genomes]
rs41315060	0.94[EUR][1000 genomes]
rs4415979	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4503768	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs45461294	0.96[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs58188999	0.91[EUR][1000 genomes]
rs59578395	0.95[EUR][1000 genomes]
rs59628570	0.85[EUR][1000 genomes]
rs6492905	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs74008647	0.91[EUR][1000 genomes]
rs74008648	0.91[EUR][1000 genomes]
rs8036035	1.00[JPT][hapmap]
rs880270	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs954152	0.93[EUR][1000 genomes]
rs985808	0.82[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][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	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

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39851000-39871800	Weak transcription	Pancreas	Pancrea
2	chr15:39854400-39870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:39857800-39870600	Weak transcription	HSMMtube	muscle
4	chr15:39862200-39863200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:39862200-39863600	Enhancers	Fetal Lung	lung
6	chr15:39862200-39863800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:39862200-39864000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:39862400-39863000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:39862400-39863400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:39862400-39863600	Enhancers	Brain Germinal Matrix	brain
11	chr15:39862600-39863400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:39862600-39865600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:39862800-39863000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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