Variant report

Variant	rs2286582
Chromosome Location	chr12:4881775-4881776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10047570	0.85[ASN][1000 genomes]
rs10431361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10431362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10774267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849125	0.86[CHB][hapmap]
rs10849126	0.85[ASN][1000 genomes]
rs10849127	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs10849129	0.85[ASN][1000 genomes]
rs10849130	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs10849131	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs10849133	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs10849137	0.89[ASN][1000 genomes]
rs10849138	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10849139	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs10849143	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11063314	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs11063318	0.85[ASN][1000 genomes]
rs11063327	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11063328	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11063331	0.91[ASN][1000 genomes]
rs12296205	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12320374	0.89[ASN][1000 genomes]
rs1468556	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs2018895	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2191157	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs2286578	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2286580	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs2286581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359466	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs2359467	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs3782740	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs3782741	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs3782742	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs3782743	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4765782	0.82[CHB][hapmap]
rs4765784	0.94[EUR][1000 genomes]
rs4766272	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs4766282	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs4766283	0.90[CHB][hapmap]
rs4766286	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs6489558	0.85[CHB][hapmap]
rs6489560	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs6489565	0.89[ASN][1000 genomes]
rs6489566	0.89[ASN][1000 genomes]
rs6489567	0.88[ASN][1000 genomes]
rs7132030	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs7295230	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7295251	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297290	0.97[ASN][1000 genomes]
rs7305387	0.89[ASN][1000 genomes]
rs7305525	0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs7311675	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311694	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7314849	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315211	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7316209	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs766504	0.88[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs766505	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7953170	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7953399	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7953482	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7966628	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7967117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970126	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7973527	0.96[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7975978	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs7976011	0.89[ASN][1000 genomes]
rs7976219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929481	0.92[ASN][1000 genomes]
rs9300304	0.86[CHB][hapmap];0.85[ASN][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	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	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
rs2286582	SLC2A14	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4869800-4884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:4873200-4881800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:4873200-4889800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:4873400-4889400	Weak transcription	Ovary	ovary
5	chr12:4877000-4885800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:4878200-4885000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:4880600-4884200	Weak transcription	Lung	lung
8	chr12:4880800-4882000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:4880800-4884400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:4880800-4884800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:4881000-4881800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:4881000-4882000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr12:4881000-4882200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:4881000-4882800	Strong transcription	Fetal Brain Female	brain
15	chr12:4881200-4882000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:4881400-4882200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:4881400-4882800	Strong transcription	Brain Germinal Matrix	brain
18	chr12:4881600-4883000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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