Variant report

Variant	rs7342673
Chromosome Location	chr15:52799364-52799365
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52796242..52797868-chr15:52798025..52800305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231169	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10518683	0.85[GIH][hapmap]
rs13329278	0.85[GIH][hapmap]
rs13329417	1.00[JPT][hapmap]
rs13329500	0.85[GIH][hapmap]
rs13329510	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669870	0.85[GIH][hapmap]
rs1669872	0.85[GIH][hapmap]
rs1693516	1.00[EUR][1000 genomes]
rs1693517	1.00[EUR][1000 genomes]
rs1693519	1.00[EUR][1000 genomes]
rs16964891	1.00[JPT][hapmap]
rs16964903	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs16964910	1.00[JPT][hapmap]
rs16964927	1.00[JPT][hapmap]
rs16964928	0.85[GIH][hapmap]
rs16964935	1.00[JPT][hapmap]
rs16964944	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs16964952	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1724577	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1724599	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1724600	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs1724602	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs2222656	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2414145	0.85[GIH][hapmap]
rs2600903	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2600904	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs28401713	1.00[ASN][1000 genomes]
rs28415472	1.00[AMR][1000 genomes]
rs28417081	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417825	1.00[EUR][1000 genomes]
rs28475475	0.85[GIH][hapmap]
rs28483042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28485735	0.87[ASN][1000 genomes]
rs28510975	1.00[ASN][1000 genomes]
rs28545705	1.00[ASN][1000 genomes]
rs28556791	1.00[EUR][1000 genomes]
rs28570350	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28578651	1.00[ASN][1000 genomes]
rs28581262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28642806	1.00[ASN][1000 genomes]
rs28663524	1.00[EUR][1000 genomes]
rs28665952	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673564	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28682547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28687913	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28699673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28761013	0.87[ASN][1000 genomes]
rs28786736	0.87[ASN][1000 genomes]
rs28795685	0.87[ASN][1000 genomes]
rs28814017	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28814321	0.87[ASN][1000 genomes]
rs28840839	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28876722	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764226	0.88[ASN][1000 genomes]
rs4499185	1.00[JPT][hapmap]
rs4774620	0.85[GIH][hapmap]
rs4774621	0.85[GIH][hapmap]
rs7163569	1.00[JPT][hapmap]
rs7163778	0.85[GIH][hapmap]
rs7166034	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7168076	1.00[JPT][hapmap]
rs7168981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169104	1.00[JPT][hapmap]
rs7169346	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7170622	1.00[JPT][hapmap]
rs7178069	1.00[JPT][hapmap]
rs7179156	1.00[JPT][hapmap]
rs73412972	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73412975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744501	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs8024412	0.85[GIH][hapmap];1.00[JPT][hapmap]
rs8035199	0.85[GIH][hapmap]
rs8041819	0.85[GIH][hapmap]
rs8042235	1.00[JPT][hapmap]
rs8042245	1.00[JPT][hapmap]
rs876549	0.85[GIH][hapmap]
rs9744852	0.85[GIH][hapmap]
rs9920195	1.00[EUR][1000 genomes]
rs9920749	1.00[JPT][hapmap]

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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv976936	chr15:52797408-52800785	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52774600-52802600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:52778600-52812400	Weak transcription	Right Ventricle	heart
3	chr15:52785000-52801200	Weak transcription	Right Atrium	heart
4	chr15:52786400-52812400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:52789600-52806600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:52792000-52801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:52792000-52815200	Weak transcription	NHLF	lung
8	chr15:52792200-52799400	Weak transcription	Brain Angular Gyrus	brain
9	chr15:52794600-52803400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:52795000-52800800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:52795000-52802800	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:52795400-52801200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:52796600-52800800	Weak transcription	HSMMtube	muscle
14	chr15:52796800-52799400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:52796800-52799600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:52796800-52801000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:52796800-52801600	Weak transcription	HSMM	muscle
18	chr15:52796800-52802200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:52796800-52803200	Weak transcription	NHDF-Ad	bronchial
20	chr15:52796800-52811200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:52796800-52819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:52796800-52820000	Weak transcription	Primary T cells from cord blood	blood
23	chr15:52797000-52815200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:52797400-52800600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:52797400-52810200	Weak transcription	Primary B cells from cord blood	blood
26	chr15:52797600-52801000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:52797600-52803200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:52797600-52819800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:52797800-52801600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:52797800-52801600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:52797800-52801600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:52797800-52802800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:52797800-52803200	Weak transcription	Adipose Nuclei	Adipose
34	chr15:52797800-52805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:52798000-52800600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:52798000-52801200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:52798000-52801600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:52798200-52803200	Weak transcription	NHEK	skin
39	chr15:52798200-52805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:52798800-52799400	Enhancers	GM12878-XiMat	blood
41	chr15:52798800-52800000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:52798800-52803800	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:52799000-52799400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:52799000-52799400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:52799000-52799800	Enhancers	Brain Substantia Nigra	brain
46	chr15:52799000-52802000	Enhancers	Brain Hippocampus Middle	brain

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