Variant report

Variant	rs1464567
Chromosome Location	chr3:49459252-49459253
allele	C/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	MTA3	chr3:49458473-49459720	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49458595-49459344	HepG2	liver:	n/a	n/a
3	CREB1	chr3:49459137-49460736	HepG2	liver:	n/a	n/a
4	MYBL2	chr3:49459239-49460787	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49458421-49459846	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:49458568-49459445	SK-N-SH	brain:	n/a	n/a
7	PML	chr3:49458468-49459582	GM12878	blood:	n/a	chr3:49458828-49458837 chr3:49458778-49458787
8	POLR2A	chr3:49459147-49460689	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:49459113-49460638	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:49459006-49460693	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49459071-49459424	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:49456096-49460980	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49459059-49459615	K562	blood:	n/a	n/a
14	POLR2A	chr3:49459211-49460593	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOS	chr3:49458618-49459252	HUVEC	blood vessel:	n/a	chr3:49458780-49458788 chr3:49458780-49458787 chr3:49458825-49458836 chr3:49458780-49458788
16	POLR2A	chr3:49459239-49460172	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49170472..49172068-chr3:49457076..49459891,2	MCF-7	breast:
2	chr3:49457686..49462880-chr3:49464384..49468098,7	MCF-7	breast:
3	chr3:49448910..49451821-chr3:49459047..49464749,5	MCF-7	breast:

Variant related genes	Relation type
NICN1-AS1	TF binding region
AMT	TF binding region
ENSG00000145029	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1050088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10640	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10865955	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130192	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130193	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130194	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11130196	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130202	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706370	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11711485	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11715915	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11716974	0.86[ASN][1000 genomes]
rs11720264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11919311	0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap]
rs11922013	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12488065	0.82[EUR][1000 genomes]
rs12489092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13078949	0.93[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs13079643	0.86[ASN][1000 genomes]
rs13096760	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1464566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1568662	0.85[EUR][1000 genomes]
rs17080528	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs17595772	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17650792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1800668	1.00[JPT][hapmap]
rs1801143	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1987628	1.00[JPT][hapmap]
rs2117939	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2312461	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878298	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34937635	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35115732	0.86[ASN][1000 genomes]
rs35701831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs3811697	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3811699	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3870336	0.91[LWK][hapmap];0.93[YRI][hapmap]
rs3870337	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3870338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3877784	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3924462	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3924463	0.83[EUR][1000 genomes]
rs4241406	0.80[EUR][1000 genomes]
rs4241408	0.83[EUR][1000 genomes]
rs4459909	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563439	0.90[EUR][1000 genomes]
rs4625	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855836	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes]
rs4855842	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855843	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855852	0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap]
rs4855855	0.82[EUR][1000 genomes]
rs4855859	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855861	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4855866	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4855873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955412	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955438	0.85[EUR][1000 genomes]
rs55957735	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59152804	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62259939	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62259942	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62261185	0.82[EUR][1000 genomes]
rs6446272	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6446274	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446277	0.86[ASN][1000 genomes]
rs6766131	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6773518	0.98[EUR][1000 genomes]
rs6779524	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6784820	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792911	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797765	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6997	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7371895	0.84[EUR][1000 genomes]
rs7373849	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621003	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7622302	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7631908	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7633271	1.00[JPT][hapmap]
rs7637665	0.81[EUR][1000 genomes]
rs7637999	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643586	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643845	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7645445	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7646366	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs885592	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814873	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9827021	1.00[JPT][hapmap]
rs9827708	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9837027	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9841110	1.00[JPT][hapmap]
rs9853683	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9858280	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9859556	0.90[ASN][1000 genomes]
rs9871380	0.94[ASN][1000 genomes]
rs9875617	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9878943	0.94[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1464567	WDR6	cis	Artery Tibial	GTEx
rs1464567	CCDC71	cis	cerebellum	SCAN
rs1464567	RBM6	cis	cerebellum	SCAN
rs1464567	WDR6	cis	cerebellum	SCAN
rs1464567	NICN1	cis	multi-tissue	Pritchard
rs1464567	WDR6	cis	Muscle Skeletal	GTEx
rs1464567	C3orf54	cis	cerebellum	SCAN
rs1464567	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs1464567	WDR6	cis	multi-tissue	Pritchard
rs1464567	NCKIPSD	cis	cerebellum	SCAN
rs1464567	BSN-AS2	cis	Muscle Skeletal	GTEx
rs1464567	RNF123	cis	cerebellum	SCAN
rs1464567	IP6K2	cis	cerebellum	SCAN
rs1464567	WDR6	cis	Nerve Tibial	GTEx
rs1464567	QRICH1	cis	parietal	SCAN
rs1464567	WDR6	cis	parietal	SCAN
rs1464567	AMT	cis	multi-tissue	Pritchard
rs1464567	WDR6	cis	lung	GTEx
rs1464567	WDR6	cis	Adipose Subcutaneous	GTEx
rs1464567	GNAI2	cis	parietal	SCAN
rs1464567	AMT	cis	Thyroid	GTEx
rs1464567	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
3	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
4	chr3:49451400-49459400	Weak transcription	Ovary	ovary
5	chr3:49454000-49459400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:49455200-49459400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:49455200-49459400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:49455200-49459600	Enhancers	Hela-S3	cervix
9	chr3:49455400-49461800	Weak transcription	Aorta	Aorta
10	chr3:49455600-49459400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:49455600-49460000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:49455600-49461600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:49455600-49461800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:49455800-49463800	Strong transcription	Dnd41	blood
16	chr3:49456400-49459600	Enhancers	Esophagus	oesophagus
17	chr3:49456800-49459400	Strong transcription	Primary T cells from cord blood	blood
18	chr3:49456800-49459400	Weak transcription	Right Atrium	heart
19	chr3:49457000-49459400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:49457000-49461600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:49457400-49459800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:49457400-49461200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:49457600-49459400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:49457600-49459400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:49457600-49465400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:49457800-49459600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:49457800-49459600	Enhancers	NHDF-Ad	bronchial
29	chr3:49457800-49460200	Weak transcription	Lung	lung
30	chr3:49457800-49461600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:49458000-49459400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49458000-49459400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:49458000-49459600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:49458000-49459600	Enhancers	HMEC	breast
35	chr3:49458000-49460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:49458000-49460600	Enhancers	Osteobl	bone
37	chr3:49458000-49460800	Genic enhancers	NHLF	lung
38	chr3:49458200-49459400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:49458200-49459400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:49458200-49459600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:49458200-49459600	Enhancers	HSMMtube	muscle
42	chr3:49458200-49460000	Weak transcription	Small Intestine	intestine
43	chr3:49458200-49460200	Enhancers	A549	lung
44	chr3:49458200-49460400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49458200-49460800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:49458200-49460800	Enhancers	NH-A	brain
47	chr3:49458200-49461800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:49458400-49459400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:49458400-49459400	Weak transcription	Fetal Brain Female	brain
50	chr3:49458400-49459600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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