Variant report

Variant	rs58012609
Chromosome Location	chr3:112465680-112465681
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	chr13:50509795..50512385-chr3:112464979..112467287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123178	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1154274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1685875	1.00[EUR][1000 genomes]
rs56728555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57140268	1.00[EUR][1000 genomes]
rs57311206	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57880608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58190520	1.00[EUR][1000 genomes]
rs58720537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59190393	1.00[EUR][1000 genomes]
rs59583995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60177418	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60266638	1.00[EUR][1000 genomes]
rs60945656	1.00[EUR][1000 genomes]
rs61564938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6802806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72946377	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72946383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72946387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72946389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72946392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645804	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112458400-112467800	Weak transcription	Stomach Mucosa	stomach
2	chr3:112458800-112467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:112459000-112467000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:112459000-112470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:112459200-112466400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:112459200-112467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:112461400-112466400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:112461400-112466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:112461800-112465800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:112462600-112468000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:112463000-112465800	Enhancers	Fetal Thymus	thymus
12	chr3:112463000-112465800	Enhancers	NHDF-Ad	bronchial
13	chr3:112463800-112465800	Enhancers	Thymus	Thymus
14	chr3:112463800-112466000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:112464200-112468000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:112464200-112469200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:112464400-112469200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:112464400-112470800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:112465000-112467000	Weak transcription	GM12878-XiMat	blood
20	chr3:112465000-112469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:112465000-112469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:112465200-112466000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:112465200-112466200	Enhancers	Osteobl	bone
24	chr3:112465400-112466000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:112465400-112466000	Flanking Active TSS	A549	lung
26	chr3:112465400-112468200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:112465600-112465800	Enhancers	HMEC	breast
28	chr3:112465600-112466000	Flanking Active TSS	K562	blood
29	chr3:112465600-112466000	Enhancers	NHLF	lung
30	chr3:112465600-112466200	Enhancers	NH-A	brain
31	chr3:112465600-112467400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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