Variant report

Variant	rs1988555
Chromosome Location	chr15:39825258-39825259
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	chr15:39823636..39827203-chr15:39871648..39874678,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1038097	0.90[EUR][1000 genomes]
rs1051442	0.86[EUR][1000 genomes]
rs10520141	0.85[EUR][1000 genomes]
rs10520143	0.80[EUR][1000 genomes]
rs1382443	0.90[EUR][1000 genomes]
rs1382444	0.90[EUR][1000 genomes]
rs16969487	0.85[EUR][1000 genomes]
rs16969491	0.85[EUR][1000 genomes]
rs17632916	0.86[EUR][1000 genomes]
rs17633107	0.86[EUR][1000 genomes]
rs17633210	0.84[EUR][1000 genomes]
rs17705806	0.84[EUR][1000 genomes]
rs17706083	0.84[EUR][1000 genomes]
rs17706179	0.84[EUR][1000 genomes]
rs1813493	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1988082	0.81[EUR][1000 genomes]
rs2228263	0.87[EUR][1000 genomes]
rs2411316	0.85[EUR][1000 genomes]
rs2618156	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2618160	0.91[EUR][1000 genomes]
rs2618161	0.90[EUR][1000 genomes]
rs2618164	0.92[EUR][1000 genomes]
rs2618165	0.92[EUR][1000 genomes]
rs2618167	0.90[EUR][1000 genomes]
rs2664123	0.91[EUR][1000 genomes]
rs2664136	0.92[EUR][1000 genomes]
rs2664137	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2664138	0.92[EUR][1000 genomes]
rs2664140	0.91[EUR][1000 genomes]
rs2664142	0.91[EUR][1000 genomes]
rs28377784	0.85[EUR][1000 genomes]
rs28549326	0.85[EUR][1000 genomes]
rs28619289	0.85[EUR][1000 genomes]
rs28653011	0.85[EUR][1000 genomes]
rs34878675	0.80[EUR][1000 genomes]
rs41315060	0.86[EUR][1000 genomes]
rs4415979	0.85[EUR][1000 genomes]
rs45461294	0.88[EUR][1000 genomes]
rs4923835	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58188999	0.84[EUR][1000 genomes]
rs59578395	0.87[EUR][1000 genomes]
rs6492905	0.87[EUR][1000 genomes]
rs74008647	0.84[EUR][1000 genomes]
rs74008648	0.85[EUR][1000 genomes]
rs880270	0.85[EUR][1000 genomes]
rs954152	0.85[EUR][1000 genomes]
rs985808	0.89[EUR][1000 genomes]
rs9972350	0.85[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:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39823600-39826400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:39823600-39835400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:39823800-39826200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:39824400-39826000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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