Variant report

Variant	rs12901989
Chromosome Location	chr15:58896060-58896061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58888706..58891622-chr15:58895276..58897701,2	MCF-7	breast:
2	chr15:58895066..58897354-chr15:59040253..59042004,2	MCF-7	breast:
3	chr15:58894443..58897022-chr15:58897229..58899718,3	K562	blood:
4	chr15:58890495..58893590-chr15:58895773..58898243,3	K562	blood:

Variant related genes	Relation type
ENSG00000239100	Chromatin interaction
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11071391	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071392	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071393	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12437457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437998	0.81[AMR][1000 genomes]
rs12438487	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12438810	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439231	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12440246	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12440267	0.84[AMR][1000 genomes]
rs12441313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs12441912	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12442451	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12591291	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12591310	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12591543	0.86[EUR][1000 genomes]
rs12592332	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12592750	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12594742	0.94[CEU][hapmap]
rs12708455	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12905110	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12905173	0.82[EUR][1000 genomes]
rs12906705	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs12906714	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907237	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908165	0.87[CEU][hapmap]
rs12908261	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12908449	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912286	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs12912327	0.81[AMR][1000 genomes]
rs12913969	0.82[CEU][hapmap]
rs12915950	0.83[EUR][1000 genomes]
rs12916010	0.83[EUR][1000 genomes]
rs12917500	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12917577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1426652	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs16940587	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16940589	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16940647	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs16940651	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17236194	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs17301864	0.88[CEU][hapmap]
rs17301905	0.85[EUR][1000 genomes]
rs17301954	0.86[AMR][1000 genomes]
rs1820548	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2052805	0.88[CEU][hapmap]
rs2242063	0.83[CEU][hapmap]
rs2242066	0.83[CEU][hapmap]
rs2303532	0.84[EUR][1000 genomes]
rs2305421	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28417700	0.87[EUR][1000 genomes]
rs28427123	0.81[AMR][1000 genomes]
rs28455654	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs28457680	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28489732	0.84[AMR][1000 genomes]
rs28542491	0.85[EUR][1000 genomes]
rs28573205	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28584993	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28600144	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28609304	0.85[EUR][1000 genomes]
rs28639679	0.82[EUR][1000 genomes]
rs28678478	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28722857	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28724298	0.82[EUR][1000 genomes]
rs28818840	0.86[AMR][1000 genomes]
rs34793995	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35499736	0.84[EUR][1000 genomes]
rs35956992	0.84[AMR][1000 genomes]
rs6074	0.88[CEU][hapmap]
rs6494030	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6494031	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6494032	0.82[EUR][1000 genomes]
rs6494033	0.94[CEU][hapmap]
rs6494034	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6494038	0.88[CEU][hapmap]
rs7163733	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7164620	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7165035	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7165402	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7166076	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7166325	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7167528	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7169205	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs7170314	0.94[CEU][hapmap]
rs7174175	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7174386	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7174414	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7178954	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7180550	0.88[EUR][1000 genomes]
rs8026668	0.85[EUR][1000 genomes]
rs8029805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8033565	0.82[EUR][1000 genomes]
rs8033691	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8035960	0.82[EUR][1000 genomes]
rs8036005	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8039791	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8040358	0.82[EUR][1000 genomes]
rs871804	0.82[CEU][hapmap]
rs9302203	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9635351	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9744518	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9920042	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920310	0.82[EUR][1000 genomes]
rs9920720	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9921024	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][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	chr15:58878000-58898400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:58878000-58900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:58878000-58900000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:58878400-58897800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:58878400-58900200	Weak transcription	Brain Substantia Nigra	brain
6	chr15:58878600-58900200	Weak transcription	NHLF	lung
7	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:58882600-58904000	Weak transcription	Gastric	stomach
11	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:58883000-58901800	Weak transcription	HUVEC	blood vessel
13	chr15:58883200-58900400	Weak transcription	Fetal Heart	heart
14	chr15:58883200-58904600	Strong transcription	HSMM	muscle
15	chr15:58883400-58900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:58883800-58896600	Weak transcription	HepG2	liver
17	chr15:58884400-58896200	Weak transcription	Lung	lung
18	chr15:58884400-58902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58885200-58897000	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:58885600-58897400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:58885800-58896200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:58885800-58906800	Weak transcription	Fetal Brain Male	brain
23	chr15:58886400-58899800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:58887200-58906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:58887400-58898200	Weak transcription	Brain Angular Gyrus	brain
26	chr15:58887600-58897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:58887800-58905200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:58888000-58906200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:58888400-58900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:58888400-58920000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:58888600-58899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:58889000-58900200	Weak transcription	Right Ventricle	heart
33	chr15:58889200-58900400	Weak transcription	NH-A	brain
34	chr15:58889600-58902000	Weak transcription	HMEC	breast
35	chr15:58889600-58904600	Weak transcription	Colonic Mucosa	Colon
36	chr15:58889600-58905200	Weak transcription	Fetal Brain Female	brain
37	chr15:58889600-58919800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:58889800-58896600	Weak transcription	Adipose Nuclei	Adipose
39	chr15:58889800-58899200	Weak transcription	Hela-S3	cervix
40	chr15:58889800-58901400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:58889800-58918800	Weak transcription	Osteobl	bone
42	chr15:58889800-58921000	Weak transcription	Ovary	ovary
43	chr15:58890000-58901400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:58890000-58904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:58890000-58906200	Weak transcription	Small Intestine	intestine
46	chr15:58890800-58896800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:58890800-58905200	Weak transcription	Brain Anterior Caudate	brain
48	chr15:58891000-58896400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:58891000-58897400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:58891000-58900000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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