Variant report

Variant	rs4788548
Chromosome Location	chr16:71655361-71655362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71652939..71655689-chr16:71657502..71661086,3	K562	blood:
2	chr16:71649063..71651732-chr16:71653397..71655968,3	MCF-7	breast:
3	chr16:71597182..71598726-chr16:71654559..71657394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140832	Chromatin interaction
ENSG00000260593	Chromatin interaction
ENSG00000252339	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1058750	1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852502	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852503	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075893	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11075894	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075901	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11075904	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[ASN][1000 genomes]
rs11075905	0.85[CEU][hapmap]
rs11862723	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923990	0.84[EUR][1000 genomes]
rs12929547	1.00[ASN][1000 genomes]
rs1364210	1.00[ASN][1000 genomes]
rs1392484	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1423983	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[ASN][1000 genomes]
rs2133773	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2334877	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap]
rs2334880	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788550	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788553	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788557	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788559	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs4788810	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788813	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788820	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788822	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788823	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788825	0.88[EUR][1000 genomes]
rs4788828	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788830	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499527	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499529	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499540	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7186112	1.00[ASN][1000 genomes]
rs7187948	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190487	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193549	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195059	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201649	0.80[EUR][1000 genomes]
rs7202479	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204967	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	1.00[ASN][1000 genomes]
rs8044144	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8051968	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052910	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053186	1.00[ASN][1000 genomes]
rs8053745	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055419	0.81[EUR][1000 genomes]
rs8058297	0.96[EUR][1000 genomes]
rs8062188	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635524	1.00[ASN][1000 genomes]
rs979790	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888756	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929840	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9929985	1.00[ASN][1000 genomes]
rs9930015	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.81[EUR][1000 genomes]
rs9931074	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934301	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934789	0.87[EUR][1000 genomes]
rs9937511	1.00[ASN][1000 genomes]
rs9939458	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4788548	PHLPP2	cis	Muscle Skeletal	GTEx
rs4788548	NRN1L	cis	parietal	SCAN
rs4788548	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4788548	CBFB	cis	parietal	SCAN
rs4788548	ZNF23	cis	parietal	SCAN
rs4788548	RANBP10	cis	parietal	SCAN
rs4788548	TMEM208	cis	parietal	SCAN
rs4788548	COG4	cis	parietal	SCAN
rs4788548	PHLPPL	cis	multi-tissue	Pritchard
rs4788548	B3GNT9	cis	parietal	SCAN
rs4788548	PHLPP2	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71650400-71658400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr16:71655200-71655400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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