Variant report

Variant	rs2054942
Chromosome Location	chr3:21698394-21698395
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11129014	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919688	0.81[CEU][hapmap];0.83[CHD][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12491669	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13100753	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1490159	0.95[ASN][1000 genomes]
rs17553820	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17618743	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1993507	0.87[CHD][hapmap]
rs2336038	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs2336039	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs34948301	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35020519	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35390603	0.96[ASN][1000 genomes]
rs3996209	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4488861	0.85[CEU][hapmap]
rs4858344	0.81[CEU][hapmap]
rs4858345	0.81[CEU][hapmap]
rs6787257	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs6790087	0.85[CEU][hapmap]
rs7628221	0.82[CEU][hapmap]
rs7644742	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834631	chr3:21612283-21763887	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1007048	chr3:21666807-21865229	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv536516	chr3:21666807-21865229	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv589896	chr3:21692393-21712269	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2054942	C3orf48	cis	parietal	SCAN
rs2054942	RPL15	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21683800-21706600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:21685600-21707200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:21687200-21701800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:21687200-21706200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:21687200-21709600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:21687400-21706800	Weak transcription	Fetal Lung	lung
7	chr3:21688000-21699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:21688000-21707000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:21695000-21703600	Weak transcription	K562	blood
10	chr3:21696600-21698800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:21696600-21713400	Weak transcription	Fetal Heart	heart
12	chr3:21696800-21713200	Weak transcription	NHDF-Ad	bronchial
13	chr3:21697000-21704400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:21697200-21706200	Weak transcription	Aorta	Aorta

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