Variant report

Variant	rs4788817
Chromosome Location	chr16:71641395-71641396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71598966..71599999-chr16:71641229..71642599,6	MCF-7	breast:
2	chr16:71634121..71636611-chr16:71640952..71642935,2	MCF-7	breast:
3	chr16:71598437..71599429-chr16:71641387..71642200,2	MCF-7	breast:
4	chr16:71639360..71642316-chr16:71645937..71648287,2	K562	blood:

Variant related genes	Relation type
ENSG00000260886	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1035545	0.91[CEU][hapmap];0.80[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10500559	0.84[EUR][1000 genomes]
rs1058747	0.92[CEU][hapmap];0.86[CHD][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11075889	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11075890	0.83[ASN][1000 genomes]
rs11075891	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11075892	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11075895	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs11539980	0.92[CEU][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs11643690	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11648240	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]
rs11648674	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11859729	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs11862798	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11866795	0.92[CHB][hapmap]
rs12051443	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12051449	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12051506	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12444484	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12447856	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs12597065	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs12920243	0.91[CEU][hapmap]
rs12926987	0.82[AMR][1000 genomes]
rs12927320	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12930206	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap]
rs12932850	0.92[CEU][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12935426	0.81[AMR][1000 genomes]
rs1392483	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs1392487	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs1477386	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1582589	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs172649	0.92[CEU][hapmap];0.86[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs172650	0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2032920	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036338	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs2113222	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2270830	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs2270831	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs2270832	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs2278031	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.82[AMR][1000 genomes]
rs2303224	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2303225	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2334879	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2334883	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2334884	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2432519	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432520	0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432524	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[EUR][1000 genomes]
rs28439683	0.82[AMR][1000 genomes]
rs28582831	0.82[AMR][1000 genomes]
rs28636800	0.80[AMR][1000 genomes]
rs310331	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34764568	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35939203	0.81[ASN][1000 genomes]
rs3751817	0.81[AMR][1000 genomes]
rs3752681	0.92[CEU][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3829537	1.00[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3925658	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4444347	0.84[CHB][hapmap]
rs4788544	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4788546	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788547	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4788549	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4788551	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs4788552	0.81[AMR][1000 genomes]
rs4788558	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs4788809	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4788812	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788814	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4788821	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4788826	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs4788827	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs57997630	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60881203	0.81[AMR][1000 genomes]
rs62053077	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62053078	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62053107	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62053108	0.83[EUR][1000 genomes]
rs7185997	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs7186717	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7188406	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7195840	0.80[ASN][1000 genomes]
rs7201754	0.84[CHB][hapmap]
rs7202288	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs7203231	0.84[CHB][hapmap]
rs7206039	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8048057	0.92[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs8048210	0.92[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8052489	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8060867	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs8061970	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs8203	0.92[CEU][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs918721	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs951939	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs9921270	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes]
rs9923264	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9923336	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9925228	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs9927336	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9927437	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9930543	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9932415	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9933961	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9936903	0.82[AMR][1000 genomes]
rs9937280	0.82[AMR][1000 genomes]
rs9939455	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs9939471	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9939658	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9940142	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9940217	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs9940707	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs9940990	0.92[CEU][hapmap];0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3430225	chr16:71633500-71661205	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4788817	PHLPPL	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71640600-71642000	Enhancers	HepG2	liver
2	chr16:71641000-71641600	Enhancers	GM12878-XiMat	blood
3	chr16:71641000-71642200	Weak transcription	A549	lung
4	chr16:71641200-71641400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:71641200-71644800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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