Variant report

Variant	rs12549299
Chromosome Location	chr8:125874959-125874960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125874240..125876735-chr8:125982573..125984700,2	MCF-7	breast:
2	chr8:125874768..125876836-chr8:125878794..125880786,2	MCF-7	breast:
3	chr8:125737801..125739852-chr8:125873745..125876555,2	MCF-7	breast:
4	chr8:125861351..125863814-chr8:125873373..125876664,3	K562	blood:
5	chr8:125739203..125742093-chr8:125872773..125876698,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170873	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10093649	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10956219	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10956220	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11774426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11784930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11987239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11990757	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs11994576	1.00[EUR][1000 genomes]
rs11994907	1.00[EUR][1000 genomes]
rs12542397	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs12547431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13272895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28446872	0.90[EUR][1000 genomes]
rs28460087	0.90[EUR][1000 genomes]
rs28597931	0.90[EUR][1000 genomes]
rs28731447	0.82[EUR][1000 genomes]
rs4870928	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871558	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871560	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6470288	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6470289	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6470290	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs6470294	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6470313	0.91[CEU][hapmap]
rs6987095	1.00[CEU][hapmap]
rs6988410	0.99[EUR][1000 genomes]
rs6992468	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7015626	0.99[EUR][1000 genomes]
rs7460031	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7463566	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7835994	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7845282	0.91[CEU][hapmap]
rs9694326	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125869400-125876400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:125869800-125878200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:125870200-125879000	Weak transcription	Fetal Heart	heart
4	chr8:125870600-125879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:125871000-125885200	Weak transcription	Esophagus	oesophagus
6	chr8:125871200-125878000	Weak transcription	NHEK	skin
7	chr8:125871600-125878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:125872600-125875400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:125873400-125877000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:125873800-125878200	Weak transcription	K562	blood
11	chr8:125873800-125880200	Weak transcription	Left Ventricle	heart
12	chr8:125874000-125875000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:125874000-125875000	Enhancers	Osteobl	bone
14	chr8:125874000-125875600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:125874400-125875400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:125874400-125884800	Weak transcription	Right Atrium	heart
17	chr8:125874600-125875200	Enhancers	NHDF-Ad	bronchial
18	chr8:125874600-125876600	Weak transcription	Ovary	ovary
19	chr8:125874600-125878600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr8:125874800-125879200	Weak transcription	Right Ventricle	heart

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