Variant report

Variant	rs16940587
Chromosome Location	chr15:58898663-58898664
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58894443..58897022-chr15:58897229..58899718,3	K562	blood:
2	chr15:58898609..58900839-chr15:58904046..58906383,2	K562	blood:
3	chr15:58897720..58899751-chr15:59040032..59042523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10851639	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11071391	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11071392	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071393	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437457	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12437998	0.83[AMR][1000 genomes]
rs12438487	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438810	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439189	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12439231	0.88[CEU][hapmap]
rs12440246	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440267	0.83[AMR][1000 genomes]
rs12441313	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs12441912	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs12442451	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591291	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591310	0.82[CEU][hapmap]
rs12591543	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592332	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592750	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594742	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs12708455	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12901989	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12905110	0.82[CEU][hapmap]
rs12905173	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906705	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906714	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12907237	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908165	0.86[CEU][hapmap]
rs12908261	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs12908449	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912286	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912327	0.83[AMR][1000 genomes]
rs12913383	0.95[CHB][hapmap]
rs12913969	0.81[CEU][hapmap]
rs12915950	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916010	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12917500	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12917577	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1365772	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1426652	0.82[CEU][hapmap]
rs16940589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940647	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940651	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17236194	0.94[CEU][hapmap]
rs17301864	0.88[CEU][hapmap]
rs17301905	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17301954	0.81[AMR][1000 genomes]
rs1820548	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869133	0.86[JPT][hapmap]
rs1869135	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2052804	0.82[AMR][1000 genomes]
rs2052805	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs2081703	0.83[ASN][1000 genomes]
rs2242063	0.83[CEU][hapmap]
rs2242066	0.82[CEU][hapmap]
rs2303532	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305421	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28417700	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28455654	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28457680	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28489732	0.83[AMR][1000 genomes]
rs28542491	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28573205	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28584993	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600144	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28609304	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28637832	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28639679	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28678478	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28722857	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28724298	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28818840	0.81[AMR][1000 genomes]
rs28852159	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34793995	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35499736	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764196	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4775084	0.84[ASN][1000 genomes]
rs6074	0.87[CEU][hapmap]
rs6494030	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494031	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494032	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494033	0.94[CEU][hapmap]
rs6494034	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs6494038	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7163733	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164620	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165035	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165259	0.83[ASN][1000 genomes]
rs7165402	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166076	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166325	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7167528	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7169205	0.82[CEU][hapmap]
rs7170314	0.94[CEU][hapmap]
rs7174175	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174386	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178954	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180550	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026668	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029805	0.94[CEU][hapmap]
rs8033565	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033691	0.88[CEU][hapmap]
rs8035960	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036005	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8039791	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040358	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs871804	0.82[CEU][hapmap]
rs9302203	0.94[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9635351	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9744518	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920042	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920310	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920720	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9921024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1551	chr15:58891639-58936580	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58878000-58900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:58878000-58900000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:58878400-58900200	Weak transcription	Brain Substantia Nigra	brain
4	chr15:58878600-58900200	Weak transcription	NHLF	lung
5	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:58882600-58904000	Weak transcription	Gastric	stomach
9	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:58883000-58901800	Weak transcription	HUVEC	blood vessel
11	chr15:58883200-58900400	Weak transcription	Fetal Heart	heart
12	chr15:58883200-58904600	Strong transcription	HSMM	muscle
13	chr15:58883400-58900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:58884400-58902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:58885800-58906800	Weak transcription	Fetal Brain Male	brain
16	chr15:58886400-58899800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:58887200-58906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:58887800-58905200	Weak transcription	Brain Germinal Matrix	brain
19	chr15:58888000-58906200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:58888400-58900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:58888400-58920000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:58888600-58899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:58889000-58900200	Weak transcription	Right Ventricle	heart
24	chr15:58889200-58900400	Weak transcription	NH-A	brain
25	chr15:58889600-58902000	Weak transcription	HMEC	breast
26	chr15:58889600-58904600	Weak transcription	Colonic Mucosa	Colon
27	chr15:58889600-58905200	Weak transcription	Fetal Brain Female	brain
28	chr15:58889600-58919800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:58889800-58899200	Weak transcription	Hela-S3	cervix
30	chr15:58889800-58901400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:58889800-58918800	Weak transcription	Osteobl	bone
32	chr15:58889800-58921000	Weak transcription	Ovary	ovary
33	chr15:58890000-58901400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:58890000-58904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:58890000-58906200	Weak transcription	Small Intestine	intestine
36	chr15:58890800-58905200	Weak transcription	Brain Anterior Caudate	brain
37	chr15:58891000-58900000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:58891000-58900400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:58891000-58906800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:58891200-58898800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:58891200-58899000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:58891800-58898800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:58892000-58902200	Weak transcription	A549	lung
45	chr15:58893000-58899200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:58893200-58898800	Strong transcription	Thymus	Thymus
47	chr15:58893200-58900000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:58893200-58902600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:58893400-58898800	Strong transcription	Fetal Lung	lung
50	chr15:58893600-58898800	Strong transcription	Primary T cells from cord blood	blood

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