Variant report

Variant	rs16962288
Chromosome Location	chr15:49578896-49578897
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49577260..49579059-chr20:45986069..45987868,2	MCF-7	breast:
2	chr15:49572675..49575460-chr15:49576891..49580443,3	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10519211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1055254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1114003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16962067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16962101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16962112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16962139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16962146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16962147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16962166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962187	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16962189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16962205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16962209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16962211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16962213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16962235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16962238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16962296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16962314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16962327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16962331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16962416	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16962425	0.84[ASN][1000 genomes]
rs17396612	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17475228	0.88[ASN][1000 genomes]
rs17476940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1835227	0.97[ASN][1000 genomes]
rs2059935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2078024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2127243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2163097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413934	0.91[EUR][1000 genomes]
rs2413958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2899437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3959659	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4360865	0.91[EUR][1000 genomes]
rs59356430	0.88[ASN][1000 genomes]
rs6493354	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7173759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7176949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7178101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7179094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7179393	0.91[EUR][1000 genomes]
rs7179907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7181656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7182449	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7183899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73394357	0.88[ASN][1000 genomes]
rs73396206	0.88[ASN][1000 genomes]
rs8025550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8028746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8029506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8031680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8033311	0.88[ASN][1000 genomes]
rs8033861	0.91[EUR][1000 genomes]
rs8035170	0.91[EUR][1000 genomes]
rs8035829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8035901	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039469	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
2	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
6	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
7	chr15:49559200-49581400	Weak transcription	Spleen	Spleen
8	chr15:49561000-49600800	Weak transcription	Pancreas	Pancrea
9	chr15:49562000-49595800	Weak transcription	HepG2	liver
10	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:49563800-49583200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:49564000-49580400	Weak transcription	Brain Substantia Nigra	brain
14	chr15:49564000-49580600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:49564000-49586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:49564000-49593600	Weak transcription	HMEC	breast
17	chr15:49564200-49593600	Weak transcription	Lung	lung
18	chr15:49565400-49583600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
20	chr15:49565600-49583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:49565800-49585200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:49566000-49585200	Weak transcription	GM12878-XiMat	blood
23	chr15:49566000-49586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:49566400-49580400	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:49566400-49595600	Weak transcription	Gastric	stomach
27	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:49569000-49580800	Weak transcription	Brain Angular Gyrus	brain
29	chr15:49572000-49583600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:49572000-49595800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:49573400-49582800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:49573600-49579800	Strong transcription	Primary T cells from cord blood	blood
34	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
35	chr15:49573800-49588400	Weak transcription	Fetal Kidney	kidney
36	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:49574000-49580400	Weak transcription	Fetal Brain Male	brain
38	chr15:49574000-49588400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:49574200-49579600	Strong transcription	Liver	Liver
40	chr15:49574200-49580400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:49574200-49589000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:49574600-49588800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:49574800-49579200	Weak transcription	NHEK	skin
44	chr15:49574800-49579800	Strong transcription	K562	blood
45	chr15:49575400-49579200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:49575600-49586800	Weak transcription	NH-A	brain
47	chr15:49575600-49587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:49575800-49579800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:49576200-49580600	Weak transcription	Aorta	Aorta
50	chr15:49576400-49581800	Weak transcription	Stomach Smooth Muscle	stomach

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