Variant report

Variant	rs4788808
Chromosome Location	chr16:71615613-71615614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr16:71615570-71615997	HepG2	liver:	n/a	n/a
2	TBP	chr16:71615533-71616356	HepG2	liver:	n/a	n/a
3	CREB1	chr16:71615371-71616066	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:71615563-71616025	HepG2	liver:	n/a	n/a
5	HNF4G	chr16:71615384-71615913	HepG2	liver:	n/a	chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615621-71615636 chr16:71615620-71615635 chr16:71615621-71615634 chr16:71615739-71615747
6	POLR2A	chr16:71615567-71615975	HepG2	liver:	n/a	n/a
7	FOXA1	chr16:71615385-71616052	HepG2	liver:	n/a	n/a
8	NFIC	chr16:71615400-71616050	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:71615462-71616036	HepG2	liver:	n/a	n/a
10	FOXA1	chr16:71615357-71616216	HepG2	liver:	n/a	n/a
11	NFIC	chr16:71615446-71616075	HepG2	liver:	n/a	n/a
12	MAFK	chr16:71615578-71615981	HepG2	liver:	n/a	chr16:71615788-71615802
13	EP300	chr16:71615449-71616021	HepG2	liver:	n/a	chr16:71615920-71615930
14	HDAC2	chr16:71615472-71616031	HepG2	liver:	n/a	chr16:71615907-71615921
15	MYBL2	chr16:71615391-71616472	HepG2	liver:	n/a	n/a
16	FOXA2	chr16:71615466-71616027	HepG2	liver:	n/a	n/a
17	MBD4	chr16:71615531-71616045	HepG2	liver:	n/a	n/a
18	TEAD4	chr16:71615411-71616077	HepG2	liver:	n/a	n/a
19	RAD21	chr16:71615529-71615973	HepG2	liver:	n/a	n/a
20	EP300	chr16:71615363-71616048	HepG2	liver:	n/a	chr16:71615920-71615930
21	MXI1	chr16:71615583-71616080	HepG2	liver:	n/a	n/a
22	NR2F2	chr16:71615483-71616089	MCF-7	breast:	n/a	n/a
23	MYBL2	chr16:71615322-71616502	HepG2	liver:	n/a	n/a
24	REST	chr16:71615481-71616042	HepG2	liver:	n/a	chr16:71615781-71615801 chr16:71615846-71615860 chr16:71615846-71615866 chr16:71615846-71615866 chr16:71615852-71615861
25	GATA3	chr16:71615608-71615834	MCF-7	breast:	n/a	n/a
26	RCOR1	chr16:71615576-71616102	HepG2	liver:	n/a	n/a
27	SP1	chr16:71615391-71616109	HepG2	liver:	n/a	n/a
28	HNF4A	chr16:71615503-71616077	HepG2	liver:	n/a	chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615621-71615634 chr16:71615739-71615747
29	RFX5	chr16:71615576-71616011	HepG2	liver:	n/a	n/a
30	HNF4A	chr16:71615478-71615900	HepG2	liver:	n/a	chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615621-71615634 chr16:71615739-71615747
31	SMC3	chr16:71615543-71615973	HepG2	liver:	n/a	n/a
32	RAD21	chr16:71615568-71615968	HepG2	liver:	n/a	n/a
33	MAFK	chr16:71615592-71615992	HepG2	liver:	n/a	chr16:71615788-71615802
34	EP300	chr16:71615549-71616009	HepG2	liver:	n/a	chr16:71615920-71615930
35	HEY1	chr16:71615416-71616036	HepG2	liver:	n/a	n/a
36	FOXA1	chr16:71615397-71616152	HepG2	liver:	n/a	n/a
37	CREB1	chr16:71615351-71616072	HepG2	liver:	n/a	n/a
38	FOXA1	chr16:71615431-71616166	HepG2	liver:	n/a	n/a
39	MAX	chr16:71615331-71616261	HepG2	liver:	n/a	n/a
40	HNF4A	chr16:71615519-71616001	HepG2	liver:	n/a	chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615620-71615635 chr16:71615622-71615634 chr16:71615620-71615635 chr16:71615621-71615634 chr16:71615739-71615747

No.	Distal block	Cell Line	Cell type
1	chr16:71614455..71616325-chr16:71619608..71621123,2	MCF-7	breast:
2	chr16:71597504..71600428-chr16:71613913..71616967,3	MCF-7	breast:
3	chr16:71611013..71613326-chr16:71614202..71616544,3	MCF-7	breast:
4	chr16:71614150..71615794-chr16:71617796..71620748,2	MCF-7	breast:

Variant related genes	Relation type
TAT	TF binding region
ENSG00000157429	Chromatin interaction
ENSG00000260886	Chromatin interaction
ENSG00000198650	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1035545	0.82[CHD][hapmap]
rs11075895	0.81[CHD][hapmap]
rs11539980	0.82[CHD][hapmap]
rs11641811	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11648240	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs11859729	0.81[CHD][hapmap]
rs11862798	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs11866559	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12444484	0.83[JPT][hapmap]
rs12447856	0.85[CHD][hapmap]
rs12930206	0.85[CHD][hapmap]
rs12932850	0.83[JPT][hapmap]
rs1392487	0.85[CHD][hapmap]
rs1544808	0.88[ASN][1000 genomes]
rs172650	0.82[CHD][hapmap]
rs1799881	0.90[ASN][1000 genomes]
rs2036338	0.84[CHD][hapmap]
rs2270830	0.85[CHD][hapmap]
rs2270831	0.85[CHD][hapmap]
rs2278031	0.85[CHD][hapmap]
rs2303226	0.90[ASN][1000 genomes]
rs2432520	0.82[CHD][hapmap]
rs34692271	0.91[ASN][1000 genomes]
rs3829537	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs4788551	0.85[CHD][hapmap]
rs4788809	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs4788815	0.97[ASN][1000 genomes]
rs4788821	0.83[JPT][hapmap]
rs7202288	0.81[CHD][hapmap]
rs72797752	0.86[ASN][1000 genomes]
rs72797754	0.87[ASN][1000 genomes]
rs72797767	0.90[ASN][1000 genomes]
rs72797770	0.90[ASN][1000 genomes]
rs72797773	0.90[ASN][1000 genomes]
rs72797783	0.92[ASN][1000 genomes]
rs72797794	0.91[ASN][1000 genomes]
rs72799815	0.82[ASN][1000 genomes]
rs72799820	0.80[ASN][1000 genomes]
rs72799830	0.81[ASN][1000 genomes]
rs8048057	0.85[CHD][hapmap]
rs8048210	0.85[CHD][hapmap]
rs8061970	0.81[CHD][hapmap]
rs904763	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs918721	0.85[CHD][hapmap]
rs9921270	0.85[CHD][hapmap]
rs9925228	0.85[CHD][hapmap]
rs9939455	0.85[CHD][hapmap]
rs9940707	0.81[CHD][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
rs4788808	NAE1	cis	cerebellum	SCAN
rs4788808	ATP6V0D1	cis	parietal	SCAN
rs4788808	SNTB2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71614000-71615800	Enhancers	Liver	Liver
2	chr16:71615400-71615800	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr16:71615600-71615800	Enhancers	A549	lung
4	chr16:71615600-71616400	Flanking Active TSS	HepG2	liver

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