Variant report

Variant	rs12442839
Chromosome Location	chr15:57224185-57224186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57222920..57225645-chr15:57236445..57240161,3	MCF-7	breast:
2	chr15:57222937..57225630-chr15:57226421..57228724,2	K562	blood:
3	chr15:57222937..57224563-chr15:57225257..57227921,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11854006	0.88[EUR][1000 genomes]
rs12437635	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438244	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12438377	0.85[AMR][1000 genomes]
rs12438464	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439149	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439266	0.84[EUR][1000 genomes]
rs12439547	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439697	0.83[AMR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440699	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12440725	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440790	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12441185	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441200	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441263	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12442069	0.85[AMR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442326	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442662	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443178	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs1647386	0.83[AMR][1000 genomes]
rs1647391	0.80[AMR][1000 genomes]
rs16977123	0.85[AMR][1000 genomes]
rs16977170	0.88[EUR][1000 genomes]
rs16977201	0.88[EUR][1000 genomes]
rs17238880	1.00[AFR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17238971	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17239020	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239068	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17239187	1.00[AFR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17819646	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819755	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819779	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17819809	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2414496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4320591	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs966807	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57224800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57212400-57224800	Weak transcription	Spleen	Spleen
3	chr15:57212400-57230400	Weak transcription	Lung	lung
4	chr15:57212400-57233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
6	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:57212800-57227200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:57213000-57227400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:57213400-57226800	Weak transcription	Brain Germinal Matrix	brain
11	chr15:57215600-57227400	Weak transcription	Fetal Brain Female	brain
12	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
13	chr15:57218600-57224800	Enhancers	Fetal Heart	heart
14	chr15:57218800-57224600	Enhancers	NHLF	lung
15	chr15:57220000-57226000	Enhancers	Fetal Intestine Large	intestine
16	chr15:57220200-57225000	Enhancers	Small Intestine	intestine
17	chr15:57220200-57226200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:57220400-57226800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr15:57220400-57236400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:57220600-57224400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:57220600-57224800	Enhancers	Brain Cingulate Gyrus	brain
22	chr15:57220800-57226200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:57221000-57224400	Enhancers	Adipose Nuclei	Adipose
24	chr15:57221000-57226000	Enhancers	Duodenum Mucosa	Duodenum
25	chr15:57221000-57226600	Enhancers	Fetal Intestine Small	intestine
26	chr15:57221200-57224600	Enhancers	Colon Smooth Muscle	Colon
27	chr15:57221200-57226600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:57221400-57224400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr15:57221400-57226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:57221400-57227200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:57221600-57224400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr15:57221600-57226400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr15:57221600-57226600	Weak transcription	HSMMtube	muscle
34	chr15:57221800-57224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:57221800-57226800	Enhancers	Brain Anterior Caudate	brain
36	chr15:57222000-57224600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:57222000-57224600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:57222000-57225200	Weak transcription	A549	lung
39	chr15:57222000-57225800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:57222200-57224200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:57222200-57224200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:57222200-57224600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr15:57222200-57224600	Enhancers	Brain Substantia Nigra	brain
44	chr15:57222200-57224600	Enhancers	Stomach Smooth Muscle	stomach
45	chr15:57222200-57224800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:57222200-57225000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:57222200-57225800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr15:57222200-57226000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr15:57222200-57226200	Weak transcription	NHEK	skin
50	chr15:57222400-57224200	Weak transcription	Gastric	stomach

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