Variant report

Variant	rs341850
Chromosome Location	chr3:21475856-21475857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12638887	0.81[CHB][hapmap]
rs13061028	0.82[CHD][hapmap]
rs2076829	0.82[CHB][hapmap]
rs341852	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs341853	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs341854	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs368255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732905	0.89[CHB][hapmap]
rs3821733	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3849537	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3849539	0.89[CHB][hapmap]
rs3860572	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[MEX][hapmap]
rs400737	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs453364	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4857999	0.94[CHB][hapmap]
rs4858000	0.94[CHB][hapmap]
rs4858002	0.94[CHB][hapmap]
rs6550607	0.94[CHB][hapmap]
rs6774929	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6787456	0.94[CHB][hapmap]
rs6787955	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797692	0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[MEX][hapmap]
rs6806788	0.88[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7611710	0.89[CHB][hapmap]
rs7614523	0.88[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7625365	0.89[CHB][hapmap]
rs7643842	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9809197	0.89[CHB][hapmap];0.94[CHD][hapmap]
rs9838377	0.85[ASN][1000 genomes]
rs9874351	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9879872	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9883841	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834630	chr3:21311619-21491327	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1006471	chr3:21385627-21596955	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	nsv1000828	chr3:21399870-21565580	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536515	chr3:21399870-21565580	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs341850	NR1D2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21458800-21483400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:21459200-21477200	Weak transcription	Fetal Lung	lung
3	chr3:21463000-21491400	Weak transcription	Aorta	Aorta
4	chr3:21474600-21478400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:21474800-21477400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:21474800-21478000	Enhancers	NHDF-Ad	bronchial
7	chr3:21475000-21476400	Enhancers	Stomach Mucosa	stomach
8	chr3:21475200-21476200	Weak transcription	Brain Germinal Matrix	brain
9	chr3:21475600-21477000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:21475800-21476400	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links