Variant report

Variant	rs4952239
Chromosome Location	chr2:31609961-31609962
allele	A/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	POLR2A	chr2:31609767-31610138	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31609265..31610186-chr2:31954524..31955433,2	MCF-7	breast:

Variant related genes	Relation type
XDH	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs185925	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206846	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs206847	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs206848	0.82[ASN][1000 genomes]
rs206849	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]
rs206851	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs206854	0.92[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs206855	0.81[CHB][hapmap]
rs206858	0.91[CHB][hapmap]
rs206859	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes]
rs206860	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs2749994	0.81[EUR][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	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	esv2762446	chr2:31521093-31610311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4952239	SLC30A6	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr2:31586000-31613000	Weak transcription	Small Intestine	intestine
5	chr2:31598400-31639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:31599600-31636600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:31602200-31613400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:31602800-31614200	Strong transcription	Liver	Liver
9	chr2:31603000-31612000	Strong transcription	Fetal Intestine Large	intestine
10	chr2:31603000-31612400	Strong transcription	Fetal Intestine Small	intestine
11	chr2:31605200-31612600	Genic enhancers	NHEK	skin
12	chr2:31606200-31610600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:31606600-31612600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:31607800-31614400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:31608800-31612000	Weak transcription	Esophagus	oesophagus
16	chr2:31609200-31610200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:31609400-31610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:31609400-31611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:31609400-31611400	Enhancers	A549	lung
20	chr2:31609400-31613200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:31609400-31621200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:31609400-31623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:31609600-31610000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:31609600-31610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:31609600-31610600	Strong transcription	HMEC	breast

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