Variant report

Variant	rs58043269
Chromosome Location	chr3:119870828-119870829
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	chr3:119812554..119815643-chr3:119870791..119873292,3	MCF-7	breast:
2	chr3:119870692..119873578-chr3:119876530..119878351,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10514764	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2319540	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2874021	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732362	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4549306	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4563433	0.82[ASN][1000 genomes]
rs56097401	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60464555	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60511075	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60845666	0.91[ASN][1000 genomes]
rs62264969	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62264981	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438565	0.93[ASN][1000 genomes]
rs72952897	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72954718	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72954719	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72954722	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72954725	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641727	0.82[ASN][1000 genomes]
rs9844063	0.89[ASN][1000 genomes]
rs9851098	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119864600-119871800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:119864800-119871600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:119866600-119871400	Weak transcription	Lung	lung
4	chr3:119866800-119871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119867000-119872000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:119867200-119871800	Enhancers	NHEK	skin
7	chr3:119867200-119872000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:119867200-119873400	Weak transcription	HSMMtube	muscle
9	chr3:119867600-119871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:119867600-119871400	Weak transcription	Spleen	Spleen
11	chr3:119867600-119872000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:119867800-119871000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:119867800-119871800	Weak transcription	Adipose Nuclei	Adipose
14	chr3:119867800-119871800	Weak transcription	Left Ventricle	heart
15	chr3:119869400-119871200	Enhancers	Fetal Intestine Small	intestine
16	chr3:119870200-119871200	Enhancers	Fetal Intestine Large	intestine
17	chr3:119870200-119871800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:119870200-119872800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:119870400-119871000	Enhancers	HepG2	liver
20	chr3:119870400-119873000	Enhancers	HMEC	breast
21	chr3:119870600-119871800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:119870800-119871000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:119870800-119871000	Enhancers	HUVEC	blood vessel
24	chr3:119870800-119871000	Enhancers	Osteobl	bone
25	chr3:119870800-119871800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:119870800-119871800	Enhancers	Hela-S3	cervix
27	chr3:119870800-119871800	Enhancers	NHDF-Ad	bronchial
28	chr3:119870800-119872200	Enhancers	Stomach Mucosa	stomach
29	chr3:119870800-119872600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:119870800-119873200	Enhancers	Placenta	Placenta

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