Variant report

Variant	rs3808607
Chromosome Location	chr8:59412924-59412925
allele	G/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	SP1	chr8:59412687-59413150	HepG2	liver:	n/a	n/a
2	ARID3A	chr8:59412484-59413478	HepG2	liver:	n/a	n/a
3	HDAC2	chr8:59412704-59413013	HepG2	liver:	n/a	chr8:59412791-59412800 chr8:59412821-59412835
4	EP300	chr8:59412602-59413180	HepG2	liver:	n/a	chr8:59412790-59412800
5	RXRA	chr8:59412707-59413012	HepG2	liver:	n/a	n/a
6	HNF4G	chr8:59412653-59412985	HepG2	liver:	n/a	chr8:59412888-59412896
7	FOXA2	chr8:59412593-59413101	HepG2	liver:	n/a	chr8:59413036-59413048
8	NR2F2	chr8:59412596-59413195	HepG2	liver:	n/a	n/a
9	FOXA1	chr8:59412490-59413199	HepG2	liver:	n/a	chr8:59413036-59413048 chr8:59412856-59412871
10	HNF4G	chr8:59412697-59413034	HepG2	liver:	n/a	chr8:59412888-59412896
11	TEAD4	chr8:59412583-59413209	HepG2	liver:	n/a	n/a
12	EP300	chr8:59412754-59413083	HepG2	liver:	n/a	chr8:59412790-59412800
13	HNF4A	chr8:59412668-59413025	HepG2	liver:	n/a	chr8:59412888-59412896
14	FOXA1	chr8:59412583-59413021	HepG2	liver:	n/a	chr8:59412856-59412871
15	MBD4	chr8:59412597-59413044	HepG2	liver:	n/a	n/a
16	FOXA2	chr8:59412382-59413216	HepG2	liver:	n/a	chr8:59413036-59413048
17	NFIC	chr8:59412621-59413086	HepG2	liver:	n/a	n/a
18	CEBPB	chr8:59412723-59412932	HepG2	liver:	n/a	n/a
19	CEBPB	chr8:59412736-59413038	HepG2	liver:	n/a	n/a
20	MAZ	chr8:59412588-59412930	HepG2	liver:	n/a	n/a
21	MAFK	chr8:59412765-59413007	HepG2	liver:	n/a	n/a
22	HNF4A	chr8:59412652-59413053	HepG2	liver:	n/a	chr8:59412888-59412896
23	NFIC	chr8:59412580-59413292	HepG2	liver:	n/a	n/a
24	EP300	chr8:59412601-59413140	HepG2	liver:	n/a	chr8:59412790-59412800
25	NR2F2	chr8:59412575-59413117	HepG2	liver:	n/a	n/a
26	MYBL2	chr8:59412467-59413218	HepG2	liver:	n/a	n/a
27	HDAC2	chr8:59412623-59413054	HepG2	liver:	n/a	chr8:59412791-59412800 chr8:59412821-59412835
28	FOXA1	chr8:59412521-59413218	HepG2	liver:	n/a	chr8:59413036-59413048 chr8:59412856-59412871
29	TCF7L2	chr8:59412700-59413492	HepG2	liver:	n/a	n/a
30	FOXA1	chr8:59412581-59412984	HepG2	liver:	n/a	chr8:59412856-59412871

Variant related genes	Relation type
ENSG00000254103	TF binding region
CYP7A1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12542233	0.88[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1457043	0.88[CEU][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2162459	0.88[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35461847	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3824260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737500	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4738686	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6996287	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8192870	0.80[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs8192871	0.94[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3808607	RAB2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59410000-59415200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr8:59411800-59413800	Enhancers	HepG2	liver
3	chr8:59411800-59418400	Weak transcription	Psoas Muscle	Psoas
4	chr8:59412600-59413200	Flanking Active TSS	Liver	Liver

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