Variant report

Variant	rs8045828
Chromosome Location	chr16:58808019-58808020
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr16:58807629-58808245	HepG2	liver:	n/a	n/a
2	TEAD4	chr16:58807745-58808176	HepG2	liver:	n/a	n/a
3	FOXA1	chr16:58807786-58808143	HepG2	liver:	n/a	n/a
4	FOXA1	chr16:58807646-58808204	HepG2	liver:	n/a	n/a
5	SP1	chr16:58807716-58808107	HepG2	liver:	n/a	n/a
6	EP300	chr16:58807726-58808089	HepG2	liver:	n/a	n/a
7	FOXA1	chr16:58807766-58808240	HepG2	liver:	n/a	n/a
8	NFIC	chr16:58807693-58808221	HepG2	liver:	n/a	n/a
9	EP300	chr16:58807883-58808112	HepG2	liver:	n/a	n/a
10	FOXA2	chr16:58807266-58808411	HepG2	liver:	n/a	n/a
11	HDAC2	chr16:58807809-58808062	HepG2	liver:	n/a	n/a
12	NR2F2	chr16:58807644-58808249	HepG2	liver:	n/a	n/a
13	RXRA	chr16:58807770-58808116	HepG2	liver:	n/a	n/a
14	FOXA1	chr16:58807766-58808063	A549	lung:	n/a	n/a
15	SMC3	chr16:58807902-58808071	HepG2	liver:	n/a	n/a
16	HDAC2	chr16:58807745-58808111	HepG2	liver:	n/a	n/a
17	FOXA2	chr16:58807825-58808121	A549	lung:	n/a	n/a
18	EP300	chr16:58807817-58808111	HepG2	liver:	n/a	n/a
19	ARID3A	chr16:58807562-58808192	HepG2	liver:	n/a	n/a
20	HNF4A	chr16:58807848-58808146	HepG2	liver:	n/a	n/a
21	CEBPB	chr16:58807843-58808104	HepG2	liver:	n/a	n/a
22	CEBPB	chr16:58807774-58808148	HepG2	liver:	n/a	n/a
23	HNF4A	chr16:58807815-58808046	HepG2	liver:	n/a	n/a
24	BHLHE40	chr16:58807890-58808029	HepG2	liver:	n/a	n/a
25	FOXA2	chr16:58807787-58808121	HepG2	liver:	n/a	n/a

No data

Variant related genes	Relation type
GEMIN8P2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11643711	0.85[ASN][1000 genomes]
rs11644269	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11859128	0.85[ASN][1000 genomes]
rs12600201	0.86[MKK][hapmap]
rs12600206	0.84[MKK][hapmap]
rs12709011	0.89[ASN][1000 genomes]
rs12919151	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12925419	0.85[ASN][1000 genomes]
rs12925537	0.85[ASN][1000 genomes]
rs12931903	0.83[ASN][1000 genomes]
rs1898234	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2013333	0.85[ASN][1000 genomes]
rs2304490	0.87[JPT][hapmap]
rs28579863	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34295929	0.83[ASN][1000 genomes]
rs4784054	0.84[ASN][1000 genomes]
rs4784980	0.89[ASN][1000 genomes]
rs6499977	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186453	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7206052	0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs73553527	0.89[ASN][1000 genomes]
rs8044439	0.85[ASN][1000 genomes]
rs8044904	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046937	0.89[ASN][1000 genomes]
rs8047097	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8047394	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8052646	0.85[ASN][1000 genomes]
rs8052824	0.89[ASN][1000 genomes]
rs8054775	0.88[ASN][1000 genomes]
rs8059778	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9937890	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv520998	chr16:58807542-58834219	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8045828	NUP93	cis	parietal	SCAN
rs8045828	CAPNS2	cis	parietal	SCAN
rs8045828	IRX5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58806600-58808400	Enhancers	Liver	Liver
2	chr16:58807600-58808600	Enhancers	HepG2	liver
3	chr16:58807800-58808200	Enhancers	A549	lung

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