Variant report

Variant	rs10002894
Chromosome Location	chr4:100141240-100141241
allele	A/C/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	SPI1	chr4:100140479-100141246	GM12878	blood:	n/a	chr4:100140841-100140848 chr4:100140844-100140853

Variant related genes	Relation type
ADH6	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1229967	1.00[ASN][1000 genomes]
rs1229969	1.00[ASN][1000 genomes]
rs1229970	1.00[ASN][1000 genomes]
rs1229976	1.00[ASN][1000 genomes]
rs1229977	1.00[ASN][1000 genomes]
rs1229982	1.00[CHB][hapmap]
rs1230019	1.00[ASN][1000 genomes]
rs1230020	1.00[ASN][1000 genomes]
rs1230022	1.00[ASN][1000 genomes]
rs1230023	0.91[ASN][1000 genomes]
rs1230025	1.00[ASN][1000 genomes]
rs1230026	1.00[ASN][1000 genomes]
rs1230027	1.00[ASN][1000 genomes]
rs1230028	1.00[ASN][1000 genomes]
rs1497375	1.00[ASN][1000 genomes]
rs1587264	0.85[ASN][1000 genomes]
rs1618572	1.00[ASN][1000 genomes]
rs1693457	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1693458	0.85[ASN][1000 genomes]
rs1789882	0.85[ASN][1000 genomes]
rs2173200	1.00[ASN][1000 genomes]
rs2646009	1.00[ASN][1000 genomes]
rs2646011	1.00[ASN][1000 genomes]
rs2851291	1.00[ASN][1000 genomes]
rs2866149	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133155	0.85[ASN][1000 genomes]
rs4147536	1.00[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4355398	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699733	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4699737	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62305755	1.00[ASN][1000 genomes]
rs6532810	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532811	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532813	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656223	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669784	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673231	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904092	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs931635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100108400-100141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:100127000-100142600	Weak transcription	Small Intestine	intestine
3	chr4:100129000-100143200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:100131400-100143000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:100140200-100141400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:100140400-100142600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:100140400-100143000	Weak transcription	Fetal Kidney	kidney
8	chr4:100140600-100143600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:100140800-100141600	Enhancers	Liver	Liver
10	chr4:100141000-100142400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:100141000-100142800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:100141000-100142800	Weak transcription	Fetal Lung	lung
13	chr4:100141000-100142800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:100141000-100143000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:100141000-100143200	Weak transcription	Stomach Mucosa	stomach
16	chr4:100141200-100142800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:100141200-100143000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:100141200-100143000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:100141200-100144000	Enhancers	HepG2	liver

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