Variant report

Variant	rs28457680
Chromosome Location	chr15:58885035-58885036
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58881400..58884258-chr15:58884787..58887600,3	K562	blood:
2	chr15:58881464..58883057-chr15:58883104..58885208,2	MCF-7	breast:
3	chr15:58877835..58880845-chr15:58881709..58886706,5	K562	blood:

Variant related genes	Relation type
ENSG00000259250	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10851639	0.83[ASN][1000 genomes]
rs11071391	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071392	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071393	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12437457	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12437955	0.89[AMR][1000 genomes]
rs12438487	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438810	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439189	0.82[ASN][1000 genomes]
rs12440091	0.88[AMR][1000 genomes]
rs12440246	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12442451	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12442956	0.88[AMR][1000 genomes]
rs12591291	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591543	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592332	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592750	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708455	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901989	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12905110	0.88[AMR][1000 genomes]
rs12905173	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906705	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906714	0.82[AMR][1000 genomes]
rs12907237	0.82[AMR][1000 genomes]
rs12908449	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12912286	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915950	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916010	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12917500	0.82[EUR][1000 genomes]
rs12917577	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1365772	0.83[ASN][1000 genomes]
rs16940587	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16940589	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16940647	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16940651	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17301905	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1820548	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869135	0.83[ASN][1000 genomes]
rs2081703	0.82[ASN][1000 genomes]
rs2303532	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305421	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28417700	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28455654	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28542491	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28549001	0.81[AMR][1000 genomes]
rs28573205	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28576281	0.88[AMR][1000 genomes]
rs28584993	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600144	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28609304	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28637832	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28639679	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28678478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28722857	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28724298	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28728383	0.80[AMR][1000 genomes]
rs28734088	0.86[AMR][1000 genomes]
rs28852159	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34793995	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35499736	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764196	0.83[ASN][1000 genomes]
rs4775084	0.83[ASN][1000 genomes]
rs6494030	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494031	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494032	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494033	0.82[AMR][1000 genomes]
rs6494034	0.81[AMR][1000 genomes]
rs6494038	0.83[AMR][1000 genomes]
rs7163733	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163939	0.81[AMR][1000 genomes]
rs7164620	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165035	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165259	0.82[ASN][1000 genomes]
rs7165402	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166076	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7166325	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7167528	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170314	0.84[AMR][1000 genomes]
rs7174175	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174386	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174414	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178954	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180550	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026668	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033565	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035960	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036005	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036448	0.89[AMR][1000 genomes]
rs8039791	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040358	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302203	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9635351	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9744518	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920042	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920310	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920720	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9921024	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58874600-58889200	Weak transcription	Small Intestine	intestine
2	chr15:58877600-58888200	Weak transcription	Placenta	Placenta
3	chr15:58877600-58888800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:58877800-58888400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:58877800-58889000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:58878000-58885600	Weak transcription	Left Ventricle	heart
7	chr15:58878000-58885800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:58878000-58885800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr15:58878000-58886200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:58878000-58886200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:58878000-58887600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr15:58878000-58887800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:58878000-58898400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:58878000-58900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:58878000-58900000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:58878200-58885600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:58878200-58885800	Weak transcription	Primary B cells from cord blood	blood
18	chr15:58878200-58886000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:58878200-58889200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:58878200-58890800	Weak transcription	Spleen	Spleen
21	chr15:58878400-58885400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:58878400-58887400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:58878400-58887600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:58878400-58888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:58878400-58890600	Weak transcription	Primary T cells from cord blood	blood
26	chr15:58878400-58897800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:58878400-58900200	Weak transcription	Brain Substantia Nigra	brain
28	chr15:58878600-58886200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr15:58878600-58888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:58878600-58889000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:58878600-58889000	Weak transcription	K562	blood
32	chr15:58878600-58890600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:58878600-58900200	Weak transcription	NHLF	lung
34	chr15:58878800-58889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:58879200-58885600	Weak transcription	Dnd41	blood
37	chr15:58879200-58893800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:58880000-58885600	Weak transcription	GM12878-XiMat	blood
39	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:58880400-58888800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:58880800-58885600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:58881600-58885800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:58881800-58885600	Weak transcription	Thymus	Thymus
45	chr15:58882400-58885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:58882600-58885800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:58882600-58886400	Weak transcription	NHEK	skin
48	chr15:58882600-58888200	Weak transcription	Hela-S3	cervix
49	chr15:58882600-58888400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:58882600-58888400	Weak transcription	HMEC	breast

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