Variant report

Variant	rs28666566
Chromosome Location	chr8:125159522-125159523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:125159165-125160832	MCF-7	breast:	n/a	chr8:125160134-125160141 chr8:125160134-125160141 chr8:125160133-125160143 chr8:125160134-125160141
2	GATA3	chr8:125159159-125160733	MCF-7	breast:	n/a	chr8:125160134-125160141 chr8:125160134-125160141 chr8:125160133-125160143 chr8:125160134-125160141
3	POLR2A	chr8:125159348-125159720	U87	brain:	n/a	n/a
4	GATA3	chr8:125159186-125159871	T-47D	breast:	n/a	n/a
5	SIN3AK20	chr8:125159080-125160758	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125152608..125156018-chr8:125157975..125161027,5	MCF-7	breast:
2	chr8:125159144..125163463-chr8:125165911..125169919,5	MCF-7	breast:
3	chr8:125080809..125082492-chr8:125157999..125159766,2	MCF-7	breast:
4	chr8:125157060..125160347-chr8:125160363..125164460,3	K562	blood:
5	chr8:125159111..125160686-chr8:125174185..125175768,2	K562	blood:
6	chr8:125150444..125155407-chr8:125156319..125163241,13	MCF-7	breast:
7	chr8:125157559..125159773-chr8:125164004..125165618,2	K562	blood:
8	chr8:125156644..125159678-chr8:125159936..125163008,3	MCF-7	breast:
9	chr8:125149183..125152556-chr8:125157722..125161369,5	MCF-7	breast:
10	chr8:125157994..125159752-chr8:125282622..125284339,2	MCF-7	breast:
11	chr8:125158434..125162428-chr8:125172218..125174995,4	MCF-7	breast:
12	chr8:125159053..125161561-chr8:125486350..125489131,2	K562	blood:

Variant related genes	Relation type
ARF1P3	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000250727	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000253227	Chromatin interaction
ENSG00000253885	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10111388	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12334966	1.00[AMR][1000 genomes]
rs16899174	1.00[AMR][1000 genomes]
rs16899177	1.00[AMR][1000 genomes]
rs28422078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28736395	1.00[AMR][1000 genomes]

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	nsv612144	chr8:125057728-125206503	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1023183	chr8:125060532-125206445	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv948556	chr8:125067187-125204721	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv831452	chr8:125099708-125259926	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125150400-125165600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:125151200-125160000	Weak transcription	Fetal Intestine Small	intestine
3	chr8:125154200-125165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr8:125154400-125159800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:125158000-125159600	Weak transcription	HUVEC	blood vessel
6	chr8:125158000-125160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:125158200-125165800	Weak transcription	Spleen	Spleen
8	chr8:125159000-125159600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:125159000-125160400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:125159000-125160600	Enhancers	HMEC	breast
11	chr8:125159000-125160800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:125159000-125160800	Enhancers	NHEK	skin
13	chr8:125159200-125160000	Enhancers	Osteobl	bone
14	chr8:125159200-125160200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr8:125159200-125160400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:125159200-125160400	Enhancers	NH-A	brain
17	chr8:125159200-125160800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:125159400-125160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:125159400-125160400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr8:125159400-125160400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:125159400-125160400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr8:125159400-125160600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr8:125159400-125160600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:125159400-125160600	Enhancers	Fetal Lung	lung
25	chr8:125159400-125160600	Flanking Active TSS	A549	lung
26	chr8:125159400-125160600	Enhancers	Hela-S3	cervix

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