Variant report

Variant	rs206849
Chromosome Location	chr2:31613249-31613250
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	STAT3	chr2:31613066-31613736	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:31613067-31613644	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:31613132-31613642	MCF10A-Er-Src	breast:	n/a	n/a
4	REST	chr2:31613109-31613673	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:31613089-31613904	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr2:31612652-31614109	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr2:31613209-31613375	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr2:31613168-31613590	Hela-S3	cervix:	n/a	n/a
9	FOS	chr2:31612984-31613704	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr2:31613153-31613529	Hela-S3	cervix:	n/a	n/a
11	MYC	chr2:31613046-31613659	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr2:31613151-31613640	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr2:31613070-31613639	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr2:31613145-31613699	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr2:31613122-31613638	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
XDH	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs185925	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs206846	0.92[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206847	0.91[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs206848	0.82[ASN][1000 genomes]
rs206854	0.92[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs206855	0.86[CHB][hapmap]
rs206858	0.95[CHB][hapmap]
rs206859	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap]
rs4952239	0.84[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs206849	SLC30A6	cis	cerebellum	SCAN
rs206849	EHD3	cis	parietal	SCAN
rs206849	DNAJC5G	cis	cerebellum	SCAN
rs206849	SYNGR2	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:31565200-31633000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:31574600-31636600	Weak transcription	Colonic Mucosa	Colon
4	chr2:31598400-31639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:31599600-31636600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:31602200-31613400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:31602800-31614200	Strong transcription	Liver	Liver
8	chr2:31607800-31614400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:31609400-31621200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:31609400-31623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:31611200-31614000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:31611800-31614400	Enhancers	HMEC	breast
13	chr2:31611800-31624000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:31612000-31618000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:31612200-31615000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:31612400-31618000	Weak transcription	Fetal Intestine Small	intestine
17	chr2:31613200-31613600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:31613200-31614200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:31613200-31615000	Enhancers	NHEK	skin
20	chr2:31613200-31616000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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