Variant report

Variant	rs1539493
Chromosome Location	chr1:151447166-151447167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11204806	0.82[EUR][1000 genomes]
rs11204820	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1196346	1.00[CEU][hapmap]
rs1196348	1.00[CEU][hapmap]
rs1196349	1.00[CEU][hapmap]
rs1196351	1.00[CEU][hapmap]
rs1196356	1.00[CEU][hapmap]
rs1196463	1.00[CEU][hapmap]
rs12566457	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12566673	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1571294	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16833248	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16833263	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16833274	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1781432	1.00[CEU][hapmap]
rs2296840	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2997072	1.00[CEU][hapmap]
rs3748549	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs3818561	1.00[CEU][hapmap]
rs4147451	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4354539	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4845778	1.00[CEU][hapmap]
rs4970916	0.82[EUR][1000 genomes]
rs4970953	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56317453	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58057716	0.82[EUR][1000 genomes]
rs59153459	0.82[EUR][1000 genomes]
rs59848815	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6587574	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6587586	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6669679	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6704126	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67750241	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633634	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72633635	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72633636	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633637	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633638	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633639	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548614	0.82[EUR][1000 genomes]
rs9729256	0.84[AMR][1000 genomes];0.82[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539493	PSMB4	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151445200-151447400	Enhancers	Fetal Heart	heart
2	chr1:151446200-151447200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:151446200-151447400	Enhancers	GM12878-XiMat	blood
4	chr1:151446200-151447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:151446200-151449800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:151446200-151450600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:151446400-151447200	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:151446400-151447200	Weak transcription	NHEK	skin
9	chr1:151446400-151447600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:151446400-151451000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:151446600-151447200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:151446600-151447200	Weak transcription	Fetal Stomach	stomach
13	chr1:151446600-151449200	Weak transcription	Right Atrium	heart
14	chr1:151446600-151450600	Weak transcription	Fetal Intestine Large	intestine
15	chr1:151446600-151450800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:151446600-151452200	Weak transcription	A549	lung
17	chr1:151447000-151447800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:151447000-151448000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links