Variant report

Variant	rs2546957
Chromosome Location	chr5:167413205-167413206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10039736	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11134483	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs11134485	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs11955430	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12522181	0.81[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12523097	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1345735	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17069646	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1821254	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1862419	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546944	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2546960	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569047	0.86[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2617956	0.90[ASN][1000 genomes]
rs2617963	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2617981	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55859018	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890434	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs730256	0.90[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs889067	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs889068	0.82[EUR][1000 genomes]
rs985650	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs992047	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	nsv830546	chr5:167303135-167456271	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167397200-167420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:167408000-167419800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:167408200-167413400	Weak transcription	Left Ventricle	heart
4	chr5:167408200-167419800	Weak transcription	NHEK	skin
5	chr5:167408400-167418400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:167408400-167419200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:167412000-167413600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:167412000-167413800	Enhancers	HepG2	liver
9	chr5:167412200-167413800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:167412400-167413800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:167412400-167413800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:167412400-167414000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:167412400-167414200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:167412600-167415000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:167412600-167415200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr5:167412800-167414000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr5:167413000-167414000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:167413200-167413600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:167413200-167413600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:167413200-167413800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:167413200-167413800	Enhancers	Right Ventricle	heart
22	chr5:167413200-167414000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:167413200-167415200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links