Variant report

Variant	rs12594222
Chromosome Location	chr15:58766108-58766109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58623181..58625459-chr15:58764481..58766715,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10518978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634902	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12591216	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592407	0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs12593736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593880	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903955	0.87[ASN][1000 genomes]
rs12904507	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12908427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910028	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16940338	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17190580	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17190587	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2414581	0.92[ASN][1000 genomes]
rs28478642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28713618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2899630	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34053638	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34225834	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34297592	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34570549	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34577128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34744603	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35633916	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35732576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35771822	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35795657	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775053	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6494009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494010	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71478667	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71478668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71478670	0.87[ASN][1000 genomes]
rs71478671	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71478672	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162384	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162603	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165752	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7169744	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7172556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174539	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029837	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041525	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
2	chr15:58759400-58768400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:58759400-58770400	Enhancers	Placenta	Placenta
4	chr15:58760400-58770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:58760600-58767000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:58761000-58767200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:58761400-58766600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:58762000-58766200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:58762600-58766600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr15:58763000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:58763800-58766600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:58764000-58770200	Enhancers	Fetal Muscle Leg	muscle
13	chr15:58764000-58770200	Enhancers	Thymus	Thymus
14	chr15:58764400-58766200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr15:58764600-58766400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:58764600-58767000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:58764600-58769600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:58764600-58769600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:58764600-58770200	Enhancers	Spleen	Spleen
20	chr15:58764800-58766400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:58764800-58766400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:58764800-58766400	Enhancers	Hela-S3	cervix
23	chr15:58764800-58766400	Enhancers	NHDF-Ad	bronchial
24	chr15:58764800-58766600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:58764800-58766600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:58764800-58769600	Enhancers	HSMMtube	muscle
27	chr15:58765000-58766200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:58765000-58766200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr15:58765000-58766200	Enhancers	Esophagus	oesophagus
30	chr15:58765000-58766200	Flanking Active TSS	Dnd41	blood
31	chr15:58765000-58766200	Flanking Active TSS	GM12878-XiMat	blood
32	chr15:58765000-58766200	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr15:58765000-58766200	Flanking Active TSS	NHEK	skin
34	chr15:58765000-58766400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:58765000-58766400	Enhancers	Fetal Kidney	kidney
36	chr15:58765000-58766400	Enhancers	K562	blood
37	chr15:58765000-58766400	Enhancers	NHLF	lung
38	chr15:58765000-58766400	Enhancers	Osteobl	bone
39	chr15:58765000-58766600	Enhancers	HSMM	muscle
40	chr15:58765000-58767600	Enhancers	HepG2	liver
41	chr15:58765000-58767800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:58765000-58768200	Enhancers	Lung	lung
43	chr15:58765000-58768400	Enhancers	Stomach Mucosa	stomach
44	chr15:58765000-58769400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:58765000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:58765000-58769600	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:58765000-58769600	Enhancers	Right Atrium	heart
48	chr15:58765000-58769800	Enhancers	Adipose Nuclei	Adipose
49	chr15:58765000-58769800	Enhancers	Pancreas	Pancrea
50	chr15:58765000-58770000	Enhancers	Primary neutrophils fromperipheralblood	blood

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