Variant report

Variant	rs574856
Chromosome Location	chr15:43460834-43460835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:43460395-43461170	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr15:43460413-43460844	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:43460407-43461301	PANC-1	pancreas:	n/a	n/a
4	TCF7L2	chr15:43460503-43461317	PANC-1	pancreas:	n/a	n/a
5	STAT3	chr15:43460419-43461025	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:43460338-43461217	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr15:43460791-43460992	Gliobla	brain:	n/a	n/a
8	FOS	chr15:43460397-43461114	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr15:43460397-43461038	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr15:43460411-43461262	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43460424..43462230-chr15:43476704..43478906,2	MCF-7	breast:

Variant related genes	Relation type
TMEM62	TF binding region
ENSG00000166946	Chromatin interaction
ENSG00000261687	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10851414	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070389	0.84[ASN][1000 genomes]
rs11070390	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629629	0.82[AFR][1000 genomes]
rs11632120	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442190	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913112	0.87[ASN][1000 genomes]
rs12913134	0.87[ASN][1000 genomes]
rs1474200	0.86[ASN][1000 genomes]
rs2056346	0.81[ASN][1000 genomes]
rs2139651	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2139652	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476342	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs489964	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs502157	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs530118	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531598	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs574531	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165861	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166467	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9635327	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43426800-43465400	Weak transcription	Psoas Muscle	Psoas
2	chr15:43427600-43475000	Weak transcription	Stomach Mucosa	stomach
3	chr15:43433400-43467600	Weak transcription	HSMM	muscle
4	chr15:43437000-43467200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:43437200-43462000	Weak transcription	Dnd41	blood
6	chr15:43440800-43476800	Weak transcription	Fetal Brain Male	brain
7	chr15:43441800-43477200	Weak transcription	HSMMtube	muscle
8	chr15:43442000-43461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:43442000-43476800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:43443000-43467600	Weak transcription	Aorta	Aorta
11	chr15:43444600-43477200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:43444800-43465400	Weak transcription	Brain Germinal Matrix	brain
13	chr15:43444800-43471600	Weak transcription	Primary T cells from cord blood	blood
14	chr15:43444800-43477000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:43444800-43477000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:43445000-43471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:43446000-43476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:43447600-43477600	Weak transcription	Small Intestine	intestine
19	chr15:43448000-43477400	Weak transcription	Ovary	ovary
20	chr15:43448200-43477200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:43449400-43467600	Weak transcription	HepG2	liver
22	chr15:43449600-43477000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:43452000-43461000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:43452800-43466200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:43453600-43462600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:43453600-43465400	Weak transcription	NHDF-Ad	bronchial
27	chr15:43453800-43461600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr15:43453800-43462000	Weak transcription	Brain Angular Gyrus	brain
29	chr15:43454000-43462400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:43457200-43461000	Weak transcription	GM12878-XiMat	blood
31	chr15:43458400-43462000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:43458400-43464400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:43460200-43461200	Strong transcription	Fetal Intestine Small	intestine
34	chr15:43460200-43462600	Enhancers	HMEC	breast
35	chr15:43460400-43461000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:43460400-43461200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:43460400-43461200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:43460400-43461200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:43460400-43461200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr15:43460400-43461200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:43460400-43461200	Strong transcription	Fetal Stomach	stomach
42	chr15:43460400-43461200	Enhancers	Fetal Thymus	thymus
43	chr15:43460400-43461200	Genic enhancers	Pancreas	Pancrea
44	chr15:43460400-43461200	Genic enhancers	Thymus	Thymus
45	chr15:43460400-43461400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:43460400-43461400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:43460400-43461400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:43460400-43461400	Genic enhancers	Esophagus	oesophagus
49	chr15:43460400-43461400	Enhancers	Placenta	Placenta
50	chr15:43460400-43461600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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