Variant report

Variant	rs11720264
Chromosome Location	chr3:49580347-49580348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49577802..49580389-chr3:49589871..49592100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226913	Chromatin interaction
ENSG00000164061	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10212296	0.85[ASN][1000 genomes]
rs1050088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10640	1.00[JPT][hapmap]
rs10865955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130192	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.84[EUR][1000 genomes]
rs11130194	0.82[EUR][1000 genomes]
rs11130196	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130202	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130203	0.94[ASN][1000 genomes]
rs11130206	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1131095	0.86[JPT][hapmap]
rs11706370	1.00[JPT][hapmap]
rs11708955	0.82[ASN][1000 genomes]
rs11709525	0.86[JPT][hapmap]
rs11711485	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11712569	0.94[ASN][1000 genomes]
rs11713474	0.86[ASN][1000 genomes]
rs11715915	1.00[JPT][hapmap]
rs11719996	0.94[ASN][1000 genomes]
rs11720458	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11919311	0.86[JPT][hapmap]
rs11922013	1.00[JPT][hapmap]
rs11926781	0.86[ASN][1000 genomes]
rs12330269	0.94[ASN][1000 genomes]
rs12488065	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636099	0.83[ASN][1000 genomes]
rs13062429	0.83[ASN][1000 genomes]
rs13079082	0.94[ASN][1000 genomes]
rs13085791	0.86[JPT][hapmap]
rs13096760	0.85[EUR][1000 genomes]
rs1464566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568662	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17080528	1.00[JPT][hapmap]
rs17650792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1800668	1.00[JPT][hapmap]
rs1801143	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1873625	0.86[JPT][hapmap]
rs1873626	0.88[JPT][hapmap]
rs1987628	1.00[JPT][hapmap]
rs2172252	0.88[JPT][hapmap]
rs2312461	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	0.86[JPT][hapmap];0.83[YRI][hapmap]
rs3197999	0.86[JPT][hapmap]
rs34196454	0.90[ASN][1000 genomes]
rs34293138	0.94[ASN][1000 genomes]
rs34363169	0.94[ASN][1000 genomes]
rs34427167	0.86[ASN][1000 genomes]
rs34762726	0.86[JPT][hapmap]
rs35261698	0.94[ASN][1000 genomes]
rs35701831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999162	0.90[ASN][1000 genomes]
rs3811697	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3811699	1.00[JPT][hapmap]
rs3870337	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3877784	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924463	0.91[EUR][1000 genomes]
rs3926569	0.90[ASN][1000 genomes]
rs4241406	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241408	0.91[EUR][1000 genomes]
rs4283605	0.86[JPT][hapmap]
rs4459909	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4855842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4855852	0.86[JPT][hapmap]
rs4855855	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855861	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855866	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855881	0.86[JPT][hapmap]
rs55957735	0.81[EUR][1000 genomes]
rs56116382	0.82[ASN][1000 genomes]
rs59152804	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62261185	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446272	1.00[JPT][hapmap]
rs67216675	0.82[ASN][1000 genomes]
rs6766131	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6766581	0.94[ASN][1000 genomes]
rs6770670	0.88[JPT][hapmap]
rs6779524	1.00[JPT][hapmap]
rs6782577	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap]
rs6784820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6787417	0.93[AFR][1000 genomes]
rs6797664	0.94[ASN][1000 genomes]
rs6803222	0.86[JPT][hapmap]
rs6997	1.00[JPT][hapmap]
rs71615484	0.90[ASN][1000 genomes]
rs7371895	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7622302	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7630869	0.82[ASN][1000 genomes]
rs7633271	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7637665	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7637999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643586	0.81[EUR][1000 genomes]
rs7643845	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645445	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7646366	1.00[JPT][hapmap]
rs885592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9812791	0.86[JPT][hapmap]
rs9814873	1.00[JPT][hapmap]
rs9818590	0.94[ASN][1000 genomes]
rs9821311	0.84[ASN][1000 genomes]
rs9827021	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9827708	0.86[JPT][hapmap]
rs9837027	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9837341	0.88[JPT][hapmap]
rs9841110	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9850072	0.94[ASN][1000 genomes]
rs9853683	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9858280	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9858418	0.85[ASN][1000 genomes]
rs9875617	1.00[JPT][hapmap]
rs9882740	0.86[JPT][hapmap]

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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11720264	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11720264	WDR6	cis	lung	GTEx
rs11720264	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11720264	WDR6	cis	Muscle Skeletal	GTEx
rs11720264	WDR6	cis	Artery Tibial	GTEx
rs11720264	WDR6	cis	Nerve Tibial	GTEx
rs11720264	AMT	cis	Thyroid	GTEx
rs11720264	WDR6	cis	Adipose Subcutaneous	GTEx
rs11720264	WDR6	cis	Whole Blood	GTEx
rs11720264	BSN-AS2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49578200-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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