Variant report

Variant	rs17115780
Chromosome Location	chr12:76229964-76229965
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76229938..76232810-chr12:76233252..76234908,2	K562	blood:
2	chr12:76227140..76230036-chr12:76423955..76426849,3	MCF-7	breast:
3	chr12:76228619..76231003-chr12:76370389..76372003,2	MCF-7	breast:
4	chr12:76217074..76218936-chr12:76228303..76230726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10431516	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10431517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10431595	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506664	0.82[JPT][hapmap]
rs11180692	0.88[JPT][hapmap]
rs11180693	0.88[JPT][hapmap]
rs11180698	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11180699	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11180700	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11180702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180704	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11180708	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180715	0.96[ASN][1000 genomes]
rs11180717	0.96[ASN][1000 genomes]
rs11180718	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.95[ASN][1000 genomes]
rs1275563	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12809551	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12810244	0.90[ASN][1000 genomes]
rs12819031	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12822358	0.94[ASN][1000 genomes]
rs12827587	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12831736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1299468	1.00[TSI][hapmap]
rs1532294	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565771	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115738	0.88[JPT][hapmap]
rs34148649	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34198570	0.84[EUR][1000 genomes]
rs35319713	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35906325	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35916241	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531531	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71460148	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71460149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937245	0.92[AMR][1000 genomes];0.96[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	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv826440	chr12:76224278-76230703	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76220400-76230000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:76225600-76230400	Weak transcription	HepG2	liver
3	chr12:76225600-76231400	Weak transcription	NHDF-Ad	bronchial
4	chr12:76225600-76234200	Weak transcription	Fetal Brain Female	brain
5	chr12:76227400-76232000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:76228000-76230000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:76228200-76232800	Enhancers	Fetal Lung	lung
8	chr12:76228600-76231000	Weak transcription	K562	blood
9	chr12:76228600-76239800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:76228600-76250000	Weak transcription	Pancreas	Pancrea
11	chr12:76229400-76230200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:76229400-76231400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:76229600-76231000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:76229600-76232200	Enhancers	Fetal Stomach	stomach
15	chr12:76229800-76230000	Enhancers	Lung	lung
16	chr12:76229800-76230600	Weak transcription	Fetal Brain Male	brain
17	chr12:76229800-76231800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:76229800-76231800	Enhancers	Fetal Muscle Leg	muscle

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