Variant report

Variant	rs12046028
Chromosome Location	chr1:224873328-224873329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10158430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458376	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495223	0.81[CEU][hapmap]
rs10495224	0.81[CEU][hapmap]
rs10799276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915692	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030079	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12030696	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12032349	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12041370	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12133496	0.81[CEU][hapmap]
rs12135077	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12144488	0.81[CEU][hapmap]
rs1499281	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1499282	0.93[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16851528	0.81[CEU][hapmap]
rs17513562	0.93[CEU][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17514252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17514370	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846501	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298736	1.00[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs3738363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738364	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3738365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653593	0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs55744530	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56121354	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56228106	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56365526	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57395227	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58715712	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59962884	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6426145	0.81[CEU][hapmap]
rs6656922	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6665737	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666840	0.81[CEU][hapmap]
rs722849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513639	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7521221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537218	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549891	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs930323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660752	1.00[CEU][hapmap]
rs9660759	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9660787	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9661696	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9661955	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9662179	0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9662190	1.00[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9725216	0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9725225	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12046028	DEGS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:224858400-224874200	Weak transcription	NH-A	brain
4	chr1:224861200-224876800	Weak transcription	Ovary	ovary
5	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
6	chr1:224864000-224876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:224868000-224874000	Weak transcription	Gastric	stomach
8	chr1:224868400-224875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:224869800-224877200	Weak transcription	Dnd41	blood
10	chr1:224871400-224876400	Strong transcription	NHDF-Ad	bronchial
11	chr1:224871800-224884600	Weak transcription	Fetal Brain Female	brain
12	chr1:224872000-224873400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:224872000-224874600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:224872600-224873400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:224872800-224876000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:224873000-224876800	Weak transcription	Fetal Brain Male	brain
17	chr1:224873000-224884800	Weak transcription	NHLF	lung
18	chr1:224873200-224873400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:224873200-224877000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links