Variant report

Variant	rs17238880
Chromosome Location	chr15:57002674-57002675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:57002606-57002791	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57000713..57002937-chr15:57007883..57010798,2	K562	blood:
2	chr15:57002294..57004303-chr15:57005932..57008123,2	MCF-7	breast:

Variant related genes	Relation type
ZNF280D	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10518872	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1087705	0.88[EUR][1000 genomes]
rs11071285	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11071286	0.92[AMR][1000 genomes]
rs12437635	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12438377	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes]
rs12438728	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12439116	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439563	0.94[EUR][1000 genomes]
rs12439586	0.88[EUR][1000 genomes]
rs12439697	0.83[EUR][1000 genomes]
rs12440006	0.94[EUR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes]
rs12440725	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12440891	1.00[AFR][1000 genomes]
rs12441746	0.89[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12442069	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes]
rs12442662	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes]
rs12443178	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12903143	0.94[EUR][1000 genomes]
rs12907983	0.94[EUR][1000 genomes]
rs1364541	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes]
rs1564557	1.00[CEU][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs1586022	0.83[EUR][1000 genomes]
rs1600829	0.94[EUR][1000 genomes]
rs1600831	0.89[EUR][1000 genomes]
rs1631905	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1647386	0.83[EUR][1000 genomes]
rs1647391	0.83[EUR][1000 genomes]
rs16977123	0.83[EUR][1000 genomes]
rs17238859	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes]
rs17819592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17819646	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes]
rs1834199	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2052641	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2161935	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2170461	0.83[EUR][1000 genomes]
rs2170462	0.88[EUR][1000 genomes]
rs2459565	0.88[EUR][1000 genomes]
rs2676178	0.88[EUR][1000 genomes]
rs2676181	0.88[EUR][1000 genomes]
rs2733231	0.83[EUR][1000 genomes]
rs2899599	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3199	0.89[MEX][hapmap]
rs4287503	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes]
rs4594195	0.83[EUR][1000 genomes]
rs4774869	0.83[EUR][1000 genomes]
rs4774885	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs480701	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493888	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176472	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74015901	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8029710	0.85[EUR][1000 genomes]
rs966807	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
2	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:56988800-57008400	Weak transcription	Fetal Heart	heart
5	chr15:56992400-57008400	Weak transcription	K562	blood
6	chr15:56992400-57010800	Weak transcription	Spleen	Spleen
7	chr15:56992400-57021800	Weak transcription	Right Ventricle	heart
8	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:56993000-57016000	Weak transcription	Pancreas	Pancrea
10	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:56993200-57007200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:56993200-57008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:56993200-57010800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:56993200-57010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:56993200-57011600	Weak transcription	HMEC	breast
16	chr15:56993400-57021600	Weak transcription	Fetal Brain Male	brain
17	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
18	chr15:56995800-57016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:56996000-57004600	Weak transcription	Esophagus	oesophagus
21	chr15:56996000-57005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:56996000-57008000	Weak transcription	Brain Angular Gyrus	brain
23	chr15:56996000-57009200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:56996000-57010800	Weak transcription	Brain Anterior Caudate	brain
25	chr15:56996000-57011000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:56996000-57011400	Weak transcription	Aorta	Aorta
27	chr15:56996000-57013000	Weak transcription	Ovary	ovary
28	chr15:56996000-57021800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:56996400-57007600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:56996400-57015800	Weak transcription	Fetal Intestine Large	intestine
31	chr15:56996400-57021600	Weak transcription	HSMMtube	muscle
32	chr15:56996400-57022600	Weak transcription	NH-A	brain
33	chr15:56996600-57011000	Weak transcription	Dnd41	blood
34	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:56997000-57003800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:56997000-57016000	Weak transcription	HSMM	muscle
37	chr15:56997200-57003400	Weak transcription	HUVEC	blood vessel
38	chr15:56997200-57015800	Weak transcription	Liver	Liver
39	chr15:56997200-57016400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:56997200-57016600	Weak transcription	Left Ventricle	heart
41	chr15:56997200-57022800	Weak transcription	Gastric	stomach
42	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
43	chr15:56997400-57010800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:56997400-57012400	Weak transcription	NHLF	lung
45	chr15:56997600-57011800	Weak transcription	NHDF-Ad	bronchial
46	chr15:56998000-57016000	Weak transcription	Fetal Lung	lung
47	chr15:56998400-57002800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:56998400-57004400	Weak transcription	Adipose Nuclei	Adipose
49	chr15:56998400-57007400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:56998400-57013800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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