Variant report

Variant	rs11128021
Chromosome Location	chr3:88139016-88139017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88109216..88112055-chr3:88137682..88139375,2	K562	blood:
2	chr3:88131832..88133596-chr3:88136802..88139464,2	K562	blood:
3	chr3:88131832..88134234-chr3:88137893..88140717,3	K562	blood:

Extended variants
information (count: 182 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs1006895	1.00[CEU][hapmap]
rs1006896	1.00[JPT][hapmap]
rs1051413	1.00[CEU][hapmap]
rs1051436	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs1063597	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs1063603	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs12493327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495016	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631689	0.84[EUR][1000 genomes]
rs13060704	0.84[EUR][1000 genomes]
rs13063511	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs13067183	0.83[EUR][1000 genomes]
rs13067419	0.99[EUR][1000 genomes]
rs13076170	0.94[CEU][hapmap]
rs13098157	0.87[CEU][hapmap]
rs13317261	0.84[EUR][1000 genomes]
rs2049817	0.94[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap]
rs2116149	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs2735556	1.00[JPT][hapmap]
rs2735559	1.00[JPT][hapmap]
rs28694532	0.80[EUR][1000 genomes]
rs3732776	1.00[CEU][hapmap]
rs3890707	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4241551	0.99[EUR][1000 genomes]
rs4257571	0.97[EUR][1000 genomes]
rs4276211	0.96[EUR][1000 genomes]
rs4276212	0.96[EUR][1000 genomes]
rs4337654	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs4368523	1.00[CEU][hapmap]
rs4374552	0.97[EUR][1000 genomes]
rs4384978	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4402954	0.90[EUR][1000 genomes]
rs4407422	0.94[EUR][1000 genomes]
rs4414876	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4429658	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4432672	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4434168	0.99[EUR][1000 genomes]
rs4438681	1.00[CEU][hapmap]
rs4485742	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4488864	0.97[EUR][1000 genomes]
rs4501136	0.97[EUR][1000 genomes]
rs4507280	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4518156	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4555548	0.97[EUR][1000 genomes]
rs4568164	0.81[EUR][1000 genomes]
rs4580585	0.97[EUR][1000 genomes]
rs4596173	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs4611846	1.00[CEU][hapmap]
rs4616670	0.98[EUR][1000 genomes]
rs4858931	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4858935	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858936	0.92[EUR][1000 genomes]
rs4858937	0.84[EUR][1000 genomes]
rs4858938	0.83[EUR][1000 genomes]
rs4858981	1.00[CEU][hapmap]
rs4858983	0.85[CEU][hapmap]
rs4858985	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs4858994	1.00[CEU][hapmap]
rs4858995	0.99[EUR][1000 genomes]
rs4858997	0.85[EUR][1000 genomes]
rs4858998	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4858999	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4859001	0.92[EUR][1000 genomes]
rs4859002	0.84[EUR][1000 genomes]
rs4859004	0.83[EUR][1000 genomes]
rs4859005	0.83[EUR][1000 genomes]
rs55744603	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55923163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60377014	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6419867	0.82[EUR][1000 genomes]
rs6551271	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6551272	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6551273	0.94[EUR][1000 genomes]
rs6551274	0.97[EUR][1000 genomes]
rs6551275	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6551277	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6551278	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6551279	0.81[EUR][1000 genomes]
rs6551280	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551281	1.00[JPT][hapmap]
rs6551282	0.93[EUR][1000 genomes]
rs6551283	0.91[EUR][1000 genomes]
rs6551284	0.92[EUR][1000 genomes]
rs6551285	0.92[EUR][1000 genomes]
rs6551286	0.92[EUR][1000 genomes]
rs6551288	0.92[EUR][1000 genomes]
rs6551289	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6551291	0.90[EUR][1000 genomes]
rs6551292	0.83[EUR][1000 genomes]
rs6551293	0.83[EUR][1000 genomes]
rs6551294	0.83[EUR][1000 genomes]
rs6551296	0.80[EUR][1000 genomes]
rs6551298	0.80[EUR][1000 genomes]
rs6762453	0.82[EUR][1000 genomes]
rs6767258	0.94[EUR][1000 genomes]
rs6771031	0.83[EUR][1000 genomes]
rs6777019	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs6778708	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781333	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6782507	0.97[EUR][1000 genomes]
rs6785359	0.92[EUR][1000 genomes]
rs6785560	0.80[EUR][1000 genomes]
rs6786788	0.99[EUR][1000 genomes]
rs6787824	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6791133	0.93[EUR][1000 genomes]
rs6792208	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6793783	0.99[EUR][1000 genomes]
rs6796355	0.96[EUR][1000 genomes]
rs6801046	0.83[EUR][1000 genomes]
rs6804818	0.99[EUR][1000 genomes]
rs6805957	0.83[EUR][1000 genomes]
rs73132515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427047	0.83[EUR][1000 genomes]
rs7427296	0.81[EUR][1000 genomes]
rs7427335	0.83[EUR][1000 genomes]
rs7427704	0.86[EUR][1000 genomes]
rs7428357	0.83[EUR][1000 genomes]
rs7429120	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7430158	0.93[EUR][1000 genomes]
rs7431074	0.82[EUR][1000 genomes]
rs7431968	1.00[JPT][hapmap]
rs7432509	0.83[EUR][1000 genomes]
rs7432838	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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7433285	0.92[EUR][1000 genomes]
rs7615585	0.83[EUR][1000 genomes]
rs7617691	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7618080	0.97[EUR][1000 genomes]
rs7618472	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs7620830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626777	0.99[EUR][1000 genomes]
rs7628689	0.91[EUR][1000 genomes]
rs7630028	0.99[EUR][1000 genomes]
rs7630240	0.96[EUR][1000 genomes]
rs7632123	0.92[EUR][1000 genomes]
rs7635996	0.99[EUR][1000 genomes]
rs7639420	0.97[EUR][1000 genomes]
rs7641173	0.90[EUR][1000 genomes]
rs7643923	0.95[EUR][1000 genomes]
rs7650707	0.97[EUR][1000 genomes]
rs7651641	0.94[EUR][1000 genomes]
rs7651999	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7652528	0.84[EUR][1000 genomes]
rs7653652	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs9310066	1.00[CEU][hapmap]
rs9310067	1.00[CEU][hapmap]
rs9310072	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9310074	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9310077	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs959049	1.00[CEU][hapmap]
rs959050	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs9809661	0.83[EUR][1000 genomes]
rs9813894	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9814057	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9826925	1.00[JPT][hapmap]
rs9831230	0.83[EUR][1000 genomes]
rs9832011	0.92[EUR][1000 genomes]
rs9834468	0.96[EUR][1000 genomes]
rs9834501	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs9836364	0.87[EUR][1000 genomes]
rs9839322	0.85[EUR][1000 genomes]
rs9841834	0.83[EUR][1000 genomes]
rs9843550	0.83[EUR][1000 genomes]
rs9845776	1.00[CEU][hapmap]
rs9847355	0.83[EUR][1000 genomes]
rs9848258	0.83[EUR][1000 genomes]
rs9849248	0.83[EUR][1000 genomes]
rs9849353	0.83[EUR][1000 genomes]
rs9854138	0.93[EUR][1000 genomes]
rs9856990	0.80[EUR][1000 genomes]
rs9861398	0.94[EUR][1000 genomes]
rs9865335	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9865578	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9865703	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9865710	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9866843	0.83[EUR][1000 genomes]
rs9868310	0.81[EUR][1000 genomes]
rs9868977	0.83[EUR][1000 genomes]
rs9876807	0.83[EUR][1000 genomes]
rs9881255	1.00[CEU][hapmap];0.99[EUR][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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11128021	ZNF654	cis	lymphoblastoid	seeQTL
rs11128021	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs11128021	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs11128021	CGGBP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:88112400-88143600	Weak transcription	HUVEC	blood vessel
3	chr3:88113200-88146200	Weak transcription	HMEC	breast
4	chr3:88116800-88139800	Weak transcription	Thymus	Thymus
5	chr3:88121800-88141800	Weak transcription	NHLF	lung
6	chr3:88125200-88163600	Weak transcription	NHDF-Ad	bronchial
7	chr3:88125800-88143800	Weak transcription	HepG2	liver
8	chr3:88128200-88139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:88128400-88142200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
11	chr3:88129400-88144200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:88129600-88180200	Weak transcription	NHEK	skin
13	chr3:88129800-88151600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:88130400-88142600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:88130600-88155000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:88131000-88139800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:88131200-88139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:88131200-88139800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:88131800-88144400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:88132200-88139800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:88132200-88140800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:88132200-88141200	Weak transcription	Spleen	Spleen
23	chr3:88132200-88147000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:88132600-88142600	Weak transcription	Brain Substantia Nigra	brain
25	chr3:88133000-88140000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:88133800-88139800	Weak transcription	Osteobl	bone
27	chr3:88133800-88155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:88134000-88141600	Weak transcription	Pancreas	Pancrea
29	chr3:88134000-88141800	Weak transcription	HSMMtube	muscle
30	chr3:88134000-88142400	Weak transcription	Psoas Muscle	Psoas
31	chr3:88134000-88176400	Weak transcription	Ovary	ovary
32	chr3:88134200-88139400	Weak transcription	K562	blood
33	chr3:88134200-88139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:88134200-88141400	Weak transcription	Brain Angular Gyrus	brain
35	chr3:88134200-88142000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:88134200-88145000	Weak transcription	Aorta	Aorta
37	chr3:88134200-88154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:88134200-88159400	Weak transcription	Fetal Heart	heart
39	chr3:88134600-88139600	Weak transcription	Adipose Nuclei	Adipose
40	chr3:88134800-88188200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:88135000-88142000	Weak transcription	Placenta	Placenta
42	chr3:88135200-88139800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:88135200-88139800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:88135200-88141000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:88135200-88142000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:88135400-88139800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:88135400-88139800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:88135400-88140400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:88135400-88140400	Strong transcription	Fetal Lung	lung
50	chr3:88135400-88140600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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