Variant report

Variant	rs12592516
Chromosome Location	chr15:33347651-33347652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:33346934..33349651-chr15:33359886..33362521,3	MCF-7	breast:
2	chr15:33347361..33349209-chr15:33358926..33360860,2	MCF-7	breast:
3	chr15:33301497..33303169-chr15:33347240..33349716,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10775202	0.80[EUR][1000 genomes]
rs11072124	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11072125	0.88[ASN][1000 genomes]
rs11072131	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072137	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072170	0.82[EUR][1000 genomes]
rs11635106	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11635199	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11636078	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636399	0.88[ASN][1000 genomes]
rs11854308	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857770	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11857793	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857821	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11857866	0.86[EUR][1000 genomes]
rs12101826	0.90[ASN][1000 genomes]
rs12440002	0.80[EUR][1000 genomes]
rs12592204	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594676	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594962	0.88[ASN][1000 genomes]
rs12595089	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16963688	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16963945	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17816711	0.81[EUR][1000 genomes]
rs1840400	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169938	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2219156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306278	0.81[EUR][1000 genomes]
rs2339178	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28446831	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28464512	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28489655	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28592093	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28592957	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676777	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28748087	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28750521	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28866011	0.88[ASN][1000 genomes]
rs34606248	0.93[EUR][1000 genomes]
rs4779604	0.81[EUR][1000 genomes]
rs4779605	0.80[EUR][1000 genomes]
rs4779606	0.81[EUR][1000 genomes]
rs61999970	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002761	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7167795	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174332	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7174340	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8028114	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8037860	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8039517	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041317	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8043116	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33324000-33356800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:33332200-33355200	Weak transcription	Gastric	stomach
3	chr15:33337000-33352000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:33337000-33358000	Weak transcription	Colonic Mucosa	Colon
5	chr15:33337600-33356800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:33337800-33356800	Weak transcription	HSMMtube	muscle
7	chr15:33338800-33355200	Weak transcription	HSMM	muscle
8	chr15:33341800-33348000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:33342200-33348000	Weak transcription	NHLF	lung
10	chr15:33344000-33356800	Weak transcription	Esophagus	oesophagus
11	chr15:33344000-33356800	Weak transcription	Lung	lung
12	chr15:33344200-33349800	Weak transcription	Placenta	Placenta
13	chr15:33345600-33348200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:33345600-33358200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:33345800-33348200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:33345800-33355200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:33345800-33355200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:33346200-33350000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr15:33346800-33348200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:33347200-33349200	Enhancers	Stomach Mucosa	stomach
21	chr15:33347600-33347800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr15:33347600-33348600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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