Variant report

Variant	rs6451239
Chromosome Location	chr5:35924091-35924092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10043573	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10053847	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10054418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10056484	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059688	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10070378	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10472264	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10472989	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10472990	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11567754	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11567761	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs13154973	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13162685	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13167136	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs13169780	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13169814	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13170810	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13172065	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1389834	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1389835	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16899999	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3822731	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4869430	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4869492	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4869674	0.86[JPT][hapmap]
rs6451229	0.88[JPT][hapmap]
rs6451234	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6451236	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6859892	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6888699	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6891095	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs6897339	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7381123	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7445819	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7710177	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7727750	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9292618	0.85[CEU][hapmap];1.00[JPT][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	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv4794	chr5:35906690-35934205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35915600-35924200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:35919600-35924200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:35920000-35924200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:35920000-35924600	Weak transcription	HSMMtube	muscle
5	chr5:35920400-35924200	Weak transcription	NHEK	skin
6	chr5:35920600-35924200	Enhancers	Dnd41	blood
7	chr5:35920600-35924400	Enhancers	Thymus	Thymus
8	chr5:35920800-35924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:35920800-35924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:35921000-35924200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:35922800-35924800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:35923000-35924400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:35923200-35925400	Enhancers	NHLF	lung
14	chr5:35923400-35924200	Enhancers	Osteobl	bone
15	chr5:35923400-35924400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:35923400-35924600	Enhancers	NHDF-Ad	bronchial
17	chr5:35923400-35924800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:35923400-35925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:35923600-35924600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:35923600-35924600	Enhancers	HMEC	breast
21	chr5:35924000-35924400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:35924000-35924600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:35924000-35924600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:35924000-35924600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr5:35924000-35924800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr5:35924000-35925000	Enhancers	Hela-S3	cervix
27	chr5:35924000-35925600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:35924000-35926800	Enhancers	Fetal Thymus	thymus

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