Variant report

Variant	rs2222656
Chromosome Location	chr15:52773023-52773024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52754471..52760057-chr15:52770956..52773396,5	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10518683	0.85[GIH][hapmap]
rs13329278	0.85[GIH][hapmap]
rs13329417	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13329500	0.85[GIH][hapmap]
rs13329510	1.00[EUR][1000 genomes];1.00[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]
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	0.87[ASN][1000 genomes]
rs28415472	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28417081	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28417825	1.00[EUR][1000 genomes]
rs28421476	0.87[ASN][1000 genomes]
rs28475475	0.85[GIH][hapmap]
rs28483042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485251	0.87[ASN][1000 genomes]
rs28485735	1.00[ASN][1000 genomes]
rs28499517	0.87[ASN][1000 genomes]
rs28510975	0.87[ASN][1000 genomes]
rs28545705	0.87[ASN][1000 genomes]
rs28556791	1.00[EUR][1000 genomes]
rs28570350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578651	0.87[ASN][1000 genomes]
rs28581262	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28613360	0.87[ASN][1000 genomes]
rs28642806	0.87[ASN][1000 genomes]
rs28663524	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28665952	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28673564	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28682547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28687913	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28699673	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28729511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28761013	1.00[ASN][1000 genomes]
rs28786736	1.00[ASN][1000 genomes]
rs28795685	1.00[ASN][1000 genomes]
rs28814017	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28814321	1.00[ASN][1000 genomes]
rs28840839	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28876722	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73412975	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7342673	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]
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];0.87[ASN][1000 genomes]
rs9920749	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels (Pyroglutamine)	23934736	GWAS catalog

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52759200-52778200	Weak transcription	Right Atrium	heart
2	chr15:52767600-52773600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52769800-52774400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:52770000-52776600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr15:52770000-52777000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:52770800-52773800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:52770800-52776400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:52771000-52773800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:52771000-52777000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr15:52771000-52778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:52771400-52776200	Enhancers	Fetal Thymus	thymus
12	chr15:52771400-52776400	Enhancers	Primary hematopoietic stem cells	blood
13	chr15:52771400-52776400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:52771800-52773800	Enhancers	Primary T cells from cord blood	blood
15	chr15:52771800-52773800	Enhancers	Thymus	Thymus
16	chr15:52771800-52774000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:52771800-52775200	Enhancers	Primary B cells from cord blood	blood
18	chr15:52771800-52776200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr15:52772000-52773600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr15:52772000-52773600	Enhancers	GM12878-XiMat	blood
21	chr15:52772000-52773800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:52772000-52773800	Enhancers	Fetal Muscle Leg	muscle
23	chr15:52772000-52774000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr15:52772000-52774600	Enhancers	Adipose Nuclei	Adipose
25	chr15:52772000-52774600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:52772000-52775400	Enhancers	HSMM	muscle
27	chr15:52772000-52775600	Enhancers	Duodenum Mucosa	Duodenum
28	chr15:52772000-52775800	Enhancers	HUVEC	blood vessel
29	chr15:52772000-52776400	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:52772000-52776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:52772000-52776800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:52772000-52776800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52772000-52777000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr15:52772000-52777000	Enhancers	NHDF-Ad	bronchial
35	chr15:52772200-52774200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:52772200-52775000	Weak transcription	Spleen	Spleen
37	chr15:52772200-52775200	Weak transcription	Left Ventricle	heart
38	chr15:52772200-52776400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr15:52772200-52776600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr15:52772200-52781600	Weak transcription	Colonic Mucosa	Colon
41	chr15:52772400-52773600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:52772400-52774000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:52772400-52775000	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:52772600-52773400	Enhancers	Rectal Smooth Muscle	rectum
45	chr15:52772600-52773600	Enhancers	Psoas Muscle	Psoas
46	chr15:52772600-52773600	Enhancers	HSMMtube	muscle
47	chr15:52772600-52773800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:52772600-52774600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:52772600-52775200	Enhancers	Brain Substantia Nigra	brain
50	chr15:52772600-52777200	Enhancers	Primary monocytes fromperipheralblood	blood

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