Variant report

Variant	rs11648240
Chromosome Location	chr16:71628274-71628275
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71599003..71601212-chr16:71626503..71628905,3	MCF-7	breast:
2	chr16:71619005..71622158-chr16:71624497..71628582,3	MCF-7	breast:
3	chr16:71617743..71620944-chr16:71623510..71629650,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260886	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1035545	0.91[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10500559	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1058747	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075889	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11075890	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11075891	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075892	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075895	0.82[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs11539980	0.92[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11643690	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11648674	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11859729	0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs11862798	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11866795	0.88[JPT][hapmap]
rs12051443	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12051449	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12051506	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12444484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12447856	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs12597065	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs12920243	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs12924258	0.80[EUR][1000 genomes]
rs12927320	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12930206	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs12930418	0.81[ASN][1000 genomes]
rs12932850	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1392483	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs1392487	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs1477386	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1582589	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs172649	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs172650	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032920	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036338	0.92[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2113222	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270830	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2270831	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2270832	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs2278031	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2303224	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2303225	0.95[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2334879	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2334883	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2334884	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432519	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432520	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432524	1.00[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28439683	0.80[EUR][1000 genomes]
rs310331	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34161748	0.80[EUR][1000 genomes]
rs34764568	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35939203	0.91[ASN][1000 genomes]
rs3752681	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829537	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3925658	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4444347	0.89[JPT][hapmap]
rs4788544	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4788546	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788547	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788549	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4788551	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs4788558	0.92[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs4788808	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs4788809	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4788812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788814	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788817	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788821	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788826	0.91[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4788827	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57997630	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62053077	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62053078	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62053107	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62053108	0.83[EUR][1000 genomes]
rs7185997	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs7186717	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7188406	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7195840	0.90[ASN][1000 genomes]
rs7201754	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7202288	0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7206039	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8048057	0.92[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8048210	0.92[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8052489	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8060867	0.95[CEU][hapmap];0.94[JPT][hapmap]
rs8061970	0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs8203	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs918721	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs951939	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs979789	0.93[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9921270	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs9923264	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9923336	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9925228	0.92[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs9927336	0.81[EUR][1000 genomes]
rs9927437	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9930543	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9932415	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9933961	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936903	0.80[EUR][1000 genomes]
rs9937280	0.80[EUR][1000 genomes]
rs9939455	0.92[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs9939471	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9939658	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9940142	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9940217	0.91[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs9940707	0.82[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11648240	ZNF23	cis	parietal	SCAN
rs11648240	B3GNT9	cis	parietal	SCAN
rs11648240	PHLPPL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71627200-71628600	Flanking Active TSS	HepG2	liver
2	chr16:71627400-71630400	Enhancers	Liver	Liver
3	chr16:71627800-71628400	Enhancers	Gastric	stomach

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