Variant report

Variant	rs7188406
Chromosome Location	chr16:71622207-71622208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71598017..71601337-chr16:71621036..71625062,4	MCF-7	breast:
2	chr16:71620059..71623986-chr16:71624555..71628126,4	K562	blood:

Variant related genes	Relation type
ENSG00000260886	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1035545	0.89[GIH][hapmap]
rs1058747	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs10775326	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11075889	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11075890	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11075891	0.93[ASN][1000 genomes]
rs11075892	0.92[ASN][1000 genomes]
rs11075895	0.92[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11539980	0.87[GIH][hapmap]
rs11643690	0.92[ASN][1000 genomes]
rs11647873	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11648240	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]
rs11859729	0.96[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11862798	0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs11865683	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11866795	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs12444484	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs12447856	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12923644	0.82[EUR][1000 genomes]
rs12928187	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12930206	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12930418	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12932850	0.93[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs13380425	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1392487	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs1477386	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs172649	0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.89[ASN][1000 genomes]
rs172650	0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[ASN][1000 genomes]
rs2032920	0.96[ASN][1000 genomes]
rs2036338	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs2113222	0.93[ASN][1000 genomes]
rs2270830	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs2270831	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs2278031	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs2334879	0.91[ASN][1000 genomes]
rs2334883	0.92[ASN][1000 genomes]
rs2334884	0.90[ASN][1000 genomes]
rs2335716	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2432519	0.93[ASN][1000 genomes]
rs2432520	0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs2432524	0.94[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs310331	0.92[ASN][1000 genomes]
rs34764568	0.89[ASN][1000 genomes]
rs35939203	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752681	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs3829537	0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs3886515	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4444347	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs4788544	0.90[ASN][1000 genomes]
rs4788546	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4788547	0.94[ASN][1000 genomes]
rs4788551	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs4788558	0.82[CHD][hapmap];0.84[GIH][hapmap]
rs4788809	0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs4788812	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs4788814	0.94[ASN][1000 genomes]
rs4788817	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs4788821	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs62053077	0.92[ASN][1000 genomes]
rs62053078	0.92[ASN][1000 genomes]
rs7186717	0.92[ASN][1000 genomes]
rs7186859	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7187877	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7191593	0.83[EUR][1000 genomes]
rs7195840	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7196498	0.81[EUR][1000 genomes]
rs7201754	0.96[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7202288	0.96[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7203168	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7203216	0.81[EUR][1000 genomes]
rs7206039	0.92[ASN][1000 genomes]
rs8048057	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs8048210	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs8053070	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8056823	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8061613	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8061970	0.96[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8063535	0.82[EUR][1000 genomes]
rs8203	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs918721	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs979789	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9921270	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs9923264	0.90[ASN][1000 genomes]
rs9923336	0.91[ASN][1000 genomes]
rs9925228	0.82[CHD][hapmap];0.89[GIH][hapmap]
rs9930543	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9932415	0.92[ASN][1000 genomes]
rs9933961	0.92[ASN][1000 genomes]
rs9939455	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs9939471	0.83[ASN][1000 genomes]
rs9939658	0.89[ASN][1000 genomes]
rs9940142	0.90[ASN][1000 genomes]
rs9940707	0.89[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][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
rs7188406	PHLPP2	cis	cerebellum	SCAN
rs7188406	TMED6	cis	parietal	SCAN
rs7188406	CHTF8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71620200-71624200	Weak transcription	Liver	Liver
2	chr16:71621800-71624200	Weak transcription	HepG2	liver

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