Variant report

Variant	rs17080528
Chromosome Location	chr3:49389842-49389843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49387116..49389894-chr3:49449590..49451097,2	K562	blood:
2	chr3:49376884..49378442-chr3:49388681..49390711,2	MCF-7	breast:
3	chr3:49388313..49390760-chr3:49397473..49400161,2	K562	blood:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1050088	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1050450	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10865955	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11130192	1.00[JPT][hapmap]
rs11130199	0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711485	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11711536	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712569	0.80[AMR][1000 genomes]
rs11713474	0.81[AMR][1000 genomes]
rs11715915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11716974	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719996	0.83[AMR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11922013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12330269	0.83[AMR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs13078949	0.85[GIH][hapmap]
rs13079082	0.82[AMR][1000 genomes]
rs13079643	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13086611	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13087851	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464566	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1464567	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1464568	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1568661	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17595772	0.94[ASN][1000 genomes]
rs17650792	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1800668	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117939	0.90[ASN][1000 genomes]
rs2878298	0.94[ASN][1000 genomes]
rs34196454	0.80[AMR][1000 genomes]
rs34293138	0.83[AMR][1000 genomes]
rs34363169	0.83[AMR][1000 genomes]
rs34588335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35115732	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35169793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261698	0.85[AMR][1000 genomes]
rs35701831	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3811697	0.81[AMR][1000 genomes]
rs3811699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870338	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3924462	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3926569	0.82[AMR][1000 genomes]
rs4625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs4855839	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap]
rs4855859	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855864	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855873	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855877	1.00[JPT][hapmap]
rs4955412	0.94[ASN][1000 genomes]
rs4955438	0.82[ASN][1000 genomes]
rs62259939	0.94[ASN][1000 genomes]
rs62259942	0.83[ASN][1000 genomes]
rs6446264	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446272	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446277	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67216675	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67485053	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs6766581	0.83[AMR][1000 genomes]
rs6779524	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6784820	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6792911	0.82[ASN][1000 genomes]
rs6793308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797664	0.83[AMR][1000 genomes]
rs6797765	0.94[ASN][1000 genomes]
rs6809216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71324962	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7373849	0.87[ASN][1000 genomes]
rs7621003	0.94[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes]
rs7623659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631908	0.88[ASN][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]
rs7637999	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7643586	0.82[ASN][1000 genomes]
rs7646366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7648841	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885592	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9818590	0.85[AMR][1000 genomes]
rs9821311	0.85[AMR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs9837027	0.81[AMR][1000 genomes]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9850072	0.83[AMR][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs9858280	0.81[AMR][1000 genomes]
rs9858418	0.82[AMR][1000 genomes]
rs9859556	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9871380	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9878943	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs17080528	CISH	cis	parietal	SCAN
rs17080528	RNF123	cis	parietal	SCAN
rs17080528	IP6K2	cis	cerebellum	SCAN
rs17080528	PARP3	cis	parietal	SCAN
rs17080528	RBM6	cis	cerebellum	SCAN
rs17080528	AMT	cis	parietal	SCAN
rs17080528	FAM212A	cis	Muscle Skeletal	GTEx
rs17080528	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs17080528	NICN1	cis	cerebellum	SCAN
rs17080528	RNF123	cis	cerebellum	SCAN
rs17080528	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs17080528	ZNF589	cis	parietal	SCAN
rs17080528	GPX1	cis	parietal	SCAN
rs17080528	KDM5B	trans	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49390000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
4	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
5	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
6	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:49383200-49391800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:49383200-49392400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:49383400-49391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:49384600-49392000	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:49384600-49392400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:49384800-49391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:49385800-49390200	Enhancers	Fetal Intestine Large	intestine
14	chr3:49386400-49390200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:49386400-49390800	Enhancers	Adipose Nuclei	Adipose
18	chr3:49386400-49390800	Enhancers	K562	blood
19	chr3:49386800-49390400	Enhancers	Placenta	Placenta
20	chr3:49387000-49393000	Weak transcription	Aorta	Aorta
21	chr3:49387200-49391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:49387200-49392800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:49387400-49392800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:49387400-49393000	Weak transcription	Right Ventricle	heart
25	chr3:49387400-49393800	Weak transcription	Gastric	stomach
26	chr3:49387600-49390800	Enhancers	Primary B cells from cord blood	blood
27	chr3:49387800-49390000	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:49387800-49393000	Weak transcription	Dnd41	blood
29	chr3:49388000-49390800	Enhancers	Esophagus	oesophagus
30	chr3:49388000-49391400	Enhancers	GM12878-XiMat	blood
31	chr3:49388200-49390200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:49388200-49390200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:49388200-49390200	Enhancers	Liver	Liver
34	chr3:49388200-49390400	Enhancers	HMEC	breast
35	chr3:49388200-49390600	Enhancers	HSMM	muscle
36	chr3:49388200-49390800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:49388200-49390800	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:49388200-49390800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:49388200-49390800	Enhancers	NHLF	lung
40	chr3:49388200-49390800	Enhancers	Osteobl	bone
41	chr3:49388400-49390200	Enhancers	Brain Anterior Caudate	brain
42	chr3:49388400-49390600	Enhancers	NHEK	skin
43	chr3:49388400-49390800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:49388400-49392600	Weak transcription	Lung	lung
45	chr3:49388400-49393000	Weak transcription	Colonic Mucosa	Colon
46	chr3:49388600-49390800	Enhancers	HUVEC	blood vessel
47	chr3:49388800-49390000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr3:49388800-49390200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:49388800-49390200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:49388800-49390400	Enhancers	Stomach Mucosa	stomach

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