Variant report

Variant	rs1586038
Chromosome Location	chr12:40475482-40475483
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005956	0.83[JPT][hapmap]
rs10506140	0.83[JPT][hapmap]
rs10747971	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs10747989	0.86[YRI][hapmap]
rs10784338	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10784353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784356	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784359	0.89[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10784369	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877891	0.92[JPT][hapmap]
rs10877990	0.88[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10878031	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878049	0.85[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10878089	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174609	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs11174670	0.82[ASN][1000 genomes]
rs11175024	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12813098	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12823555	0.81[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1482281	0.80[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1600866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813122	0.80[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs2128277	0.92[JPT][hapmap]
rs2404352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896825	0.92[JPT][hapmap]
rs2896905	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs3925535	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625545	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4767960	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768200	0.90[JPT][hapmap]
rs4768204	0.83[JPT][hapmap]
rs530602	0.92[JPT][hapmap]
rs550669	0.92[JPT][hapmap]
rs6581504	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6650226	0.80[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs716268	0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313209	0.92[JPT][hapmap]
rs7313231	0.83[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs7953129	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7954875	0.82[ASN][1000 genomes]
rs7959498	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs7960662	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964150	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs7970812	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs9669240	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1586038	SLC2A13	cis	parietal	SCAN
rs1586038	AC079630.2	cis	Esophagus Mucosa	GTEx
rs1586038	ZCRB1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40453800-40487400	Weak transcription	Left Ventricle	heart
2	chr12:40464400-40493200	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:40473400-40475800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:40474000-40476600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:40474200-40476200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:40474400-40497000	Weak transcription	Ovary	ovary
9	chr12:40474800-40476000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:40474800-40480600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:40475200-40475800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:40475400-40483000	Weak transcription	Adipose Nuclei	Adipose
13	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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