Variant report

Variant	rs1800759
Chromosome Location	chr4:100065509-100065510
allele	A/C
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	FOXA1	chr4:100065178-100065661	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:100065188-100065600	HepG2	liver:	n/a	n/a
3	ELF1	chr4:100065306-100065641	HepG2	liver:	n/a	n/a
4	E2F4	chr4:100065456-100065560	MCF10A-Er-Src	breast:	n/a	n/a
5	SP1	chr4:100065308-100065651	HepG2	liver:	n/a	n/a
6	STAT3	chr4:100065326-100065526	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr4:100065340-100065623	HepG2	liver:	n/a	chr4:100065485-100065498 chr4:100065485-100065498 chr4:100065485-100065496
8	CEBPB	chr4:100065319-100065653	HepG2	liver:	n/a	chr4:100065485-100065498 chr4:100065485-100065498 chr4:100065485-100065496
9	RCOR1	chr4:100065343-100065615	HepG2	liver:	n/a	n/a
10	POLR2A	chr4:100065213-100065570	HepG2	liver:	n/a	n/a
11	NFIC	chr4:100065244-100065618	HepG2	liver:	n/a	n/a
12	TEAD4	chr4:100065085-100065817	HepG2	liver:	n/a	n/a
13	HNF4A	chr4:100065370-100065641	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:100065029-100065597	HepG2	liver:	n/a	n/a
15	FOS	chr4:100065393-100065545	MCF10A-Er-Src	breast:	n/a	chr4:100065504-100065513 chr4:100065400-100065412
16	HEY1	chr4:100065137-100065663	HepG2	liver:	n/a	n/a
17	JUN	chr4:100065381-100065599	HepG2	liver:	n/a	chr4:100065504-100065513 chr4:100065400-100065412
18	HNF4A	chr4:100065366-100065729	HepG2	liver:	n/a	n/a
19	JUND	chr4:100065347-100065621	HepG2	liver:	n/a	chr4:100065504-100065513 chr4:100065400-100065412
20	EP300	chr4:100065135-100065752	HepG2	liver:	n/a	chr4:100065506-100065515 chr4:100065502-100065516 chr4:100065508-100065522
21	MBD4	chr4:100065080-100065580	HepG2	liver:	n/a	n/a
22	CEBPB	chr4:100065301-100065731	HepG2	liver:	n/a	chr4:100065485-100065498 chr4:100065485-100065498 chr4:100065485-100065496
23	SMC3	chr4:100065262-100065626	HepG2	liver:	n/a	n/a
24	MYBL2	chr4:100065192-100065729	HepG2	liver:	n/a	n/a
25	FOXA1	chr4:100065202-100065682	HepG2	liver:	n/a	n/a
26	MYBL2	chr4:100065042-100065797	HepG2	liver:	n/a	n/a
27	HNF4G	chr4:100065361-100065690	HepG2	liver:	n/a	n/a
28	CEBPB	chr4:100065337-100065723	HepG2	liver:	n/a	chr4:100065485-100065498 chr4:100065485-100065498 chr4:100065485-100065496
29	EP300	chr4:100065256-100065685	HepG2	liver:	n/a	chr4:100065506-100065515 chr4:100065502-100065516 chr4:100065508-100065522
30	STAT3	chr4:100065175-100065615	MCF10A-Er-Src	breast:	n/a	n/a
31	RAD21	chr4:100065269-100065571	HepG2	liver:	n/a	n/a
32	NFIC	chr4:100065161-100065801	HepG2	liver:	n/a	n/a
33	EP300	chr4:100065360-100065665	HepG2	liver:	n/a	chr4:100065506-100065515 chr4:100065502-100065516 chr4:100065508-100065522
34	CEBPB	chr4:100065361-100065625	IMR90	lung:	n/a	chr4:100065485-100065498 chr4:100065485-100065498 chr4:100065485-100065496
35	FOXA2	chr4:100065270-100065615	HepG2	liver:	n/a	n/a
36	TBP	chr4:100065265-100065629	HepG2	liver:	n/a	n/a
37	HEY1	chr4:100065082-100065636	HepG2	liver:	n/a	n/a
38	FOXA1	chr4:100065166-100065663	HepG2	liver:	n/a	n/a
39	HNF4A	chr4:100065346-100065773	HepG2	liver:	n/a	n/a
40	POLR2A	chr4:100064772-100065667	HepG2	liver:	n/a	n/a
41	ARID3A	chr4:100065108-100065911	HepG2	liver:	n/a	n/a
42	FOXA1	chr4:100065191-100065740	HepG2	liver:	n/a	n/a
43	HDAC2	chr4:100065226-100065648	HepG2	liver:	n/a	chr4:100065508-100065522

Variant related genes	Relation type
ADH4	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10022174	1.00[ASN][1000 genomes]
rs10026860	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1133483	0.87[ASN][1000 genomes]
rs12649136	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2156731	0.99[ASN][1000 genomes]
rs2226896	1.00[ASN][1000 genomes]
rs2602836	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2602844	0.87[ASN][1000 genomes]
rs2602874	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2924584	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs35882815	1.00[ASN][1000 genomes]
rs4148884	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57058570	0.95[ASN][1000 genomes]
rs6840413	0.98[ASN][1000 genomes]
rs6858148	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692974	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1800759	ADH5	cis	cerebellum	SCAN
rs1800759	ADH5	cis	Whole Blood	GTEx
rs1800759	RP11-696N14.1	cis	Nerve Tibial	GTEx
rs1800759	RP11-696N14.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1800759	METAP1	cis	cerebellum	SCAN
rs1800759	RP11-696N14.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100035000-100098200	Weak transcription	Ovary	ovary
2	chr4:100056800-100082600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:100062600-100065800	Active TSS	Duodenum Mucosa	Duodenum
4	chr4:100063600-100066600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:100063800-100066600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:100064000-100065800	Active TSS	Liver	Liver
7	chr4:100064000-100082600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:100064600-100066600	Enhancers	Fetal Intestine Small	intestine
9	chr4:100064800-100065600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:100065000-100065600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:100065000-100066600	Enhancers	Fetal Intestine Large	intestine
12	chr4:100065200-100065600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:100065200-100065600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:100065200-100065600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:100065200-100065600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr4:100065200-100065600	Enhancers	Fetal Lung	lung
17	chr4:100065200-100065600	Flanking Active TSS	HepG2	liver
18	chr4:100065200-100065800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:100065200-100066000	Enhancers	Adipose Nuclei	Adipose
20	chr4:100065400-100065600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr4:100065400-100066000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:100065400-100066200	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links