Variant report

Variant	rs10838739
Chromosome Location	chr11:47672743-47672744
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	chr11:47665176..47668139-chr11:47670216..47674244,3	MCF-7	breast:

Extended variants
information (count: 148 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10458915	0.87[ASN][1000 genomes]
rs1056387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs10742817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10742824	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10769285	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769288	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10769299	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10769300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10838726	0.89[JPT][hapmap]
rs10838732	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838736	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838741	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838745	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838751	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838760	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838763	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838766	0.90[ASN][1000 genomes]
rs10838767	0.87[ASN][1000 genomes]
rs10838768	0.90[ASN][1000 genomes]
rs10838769	0.90[ASN][1000 genomes]
rs10838771	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10838773	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10838774	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs10838775	0.87[ASN][1000 genomes]
rs10838776	0.87[ASN][1000 genomes]
rs10838777	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs10838782	0.83[ASN][1000 genomes]
rs10838784	0.83[ASN][1000 genomes]
rs11039280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11039329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039332	0.95[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11039336	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039337	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039354	0.81[EUR][1000 genomes]
rs11039373	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039376	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039379	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039392	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039401	0.90[ASN][1000 genomes]
rs11039402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs11039414	0.88[ASN][1000 genomes]
rs11039415	0.87[ASN][1000 genomes]
rs11039419	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11039429	0.87[ASN][1000 genomes]
rs11039431	0.83[ASN][1000 genomes]
rs11039432	0.83[ASN][1000 genomes]
rs12223593	0.80[ASN][1000 genomes]
rs12225854	0.87[ASN][1000 genomes]
rs12226431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12226590	0.81[ASN][1000 genomes]
rs12286721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12360643	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12362318	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12365079	0.80[ASN][1000 genomes]
rs12421563	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12576933	0.83[ASN][1000 genomes]
rs12577383	0.80[ASN][1000 genomes]
rs12785949	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1563820	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1563821	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2125838	0.85[ASN][1000 genomes]
rs2170815	0.83[ASN][1000 genomes]
rs2203712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2242081	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2290851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617307	0.90[ASN][1000 genomes]
rs2869534	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2869541	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2904127	0.90[ASN][1000 genomes]
rs3740699	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs3758655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816605	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.87[ASN][1000 genomes]
rs3886262	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4539273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4543938	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4752792	0.90[ASN][1000 genomes]
rs4752796	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[ASN][1000 genomes]
rs4752798	0.83[ASN][1000 genomes]
rs4752858	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752865	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60833259	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61895760	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485758	0.89[JPT][hapmap]
rs6485763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485773	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485775	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485778	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485786	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7101597	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7102205	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7105791	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7110300	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs7111509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7111576	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7111606	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7112248	0.85[ASN][1000 genomes]
rs7114011	0.93[GIH][hapmap];0.94[JPT][hapmap]
rs7114813	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs7115228	0.88[ASN][1000 genomes]
rs7116320	0.84[ASN][1000 genomes]
rs7116346	0.83[ASN][1000 genomes]
rs7116970	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7118747	0.83[ASN][1000 genomes]
rs7120548	0.89[GIH][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7122182	0.89[ASN][1000 genomes]
rs7122217	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7123952	0.87[ASN][1000 genomes]
rs7124396	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7126378	0.85[ASN][1000 genomes]
rs7129237	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7129797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131262	0.94[JPT][hapmap]
rs754434	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs7925211	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7927445	0.93[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7929014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7929725	0.83[ASN][1000 genomes]
rs7932703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7933019	0.89[JPT][hapmap]
rs7933184	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7933896	0.83[ASN][1000 genomes]
rs7935344	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7935521	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7935528	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7936948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7939420	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7941399	0.81[ASN][1000 genomes]
rs7943213	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7943464	0.83[ASN][1000 genomes]
rs7945312	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948468	0.88[ASN][1000 genomes]
rs7950674	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs7950696	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9633830	0.86[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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10838739	SLC39A13	cis	cerebellum	SCAN
rs10838739	MTCH2	cis	cerebellum	SCAN
rs10838739	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838739	NUP160	cis	multi-tissue	Pritchard
rs10838739	CRY2	cis	parietal	SCAN
rs10838739	MYBPC3	cis	multi-tissue	Pritchard
rs10838739	SPI1	cis	multi-tissue	Pritchard
rs10838739	C1QTNF4	cis	multi-tissue	Pritchard
rs10838739	FNBP4	cis	lesional skin	skin_eQTL
rs10838739		cis	Lymphoblastoid	GTEx
rs10838739	SLC35C1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47672600-47672800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:47672600-47673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:47672600-47673400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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