Variant report

Variant	rs2972394
Chromosome Location	chr5:42390038-42390039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10064323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941576	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117110	0.91[ASN][1000 genomes]
rs11738365	0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12513643	0.98[ASN][1000 genomes]
rs12514403	0.86[JPT][hapmap]
rs12515480	0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12517368	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12517931	0.98[ASN][1000 genomes]
rs12518010	0.89[ASN][1000 genomes]
rs12518274	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12520318	0.98[ASN][1000 genomes]
rs12522222	0.89[ASN][1000 genomes]
rs12522421	0.89[ASN][1000 genomes]
rs12523537	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654242	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13185872	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396768	0.91[ASN][1000 genomes]
rs1396775	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472947	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509455	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1509456	0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1509460	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1509462	1.00[JPT][hapmap]
rs1605851	0.88[ASN][1000 genomes]
rs16872537	0.94[ASN][1000 genomes]
rs16872543	0.94[ASN][1000 genomes]
rs16872564	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1858136	0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1858138	0.98[ASN][1000 genomes]
rs1876790	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1960498	0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1979994	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2036745	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2202883	0.91[ASN][1000 genomes]
rs2221712	0.91[ASN][1000 genomes]
rs2395970	0.91[ASN][1000 genomes]
rs28498583	0.89[ASN][1000 genomes]
rs28943877	0.94[ASN][1000 genomes]
rs2940912	0.93[ASN][1000 genomes]
rs2940914	0.91[ASN][1000 genomes]
rs2940917	0.82[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2940918	0.82[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2940919	0.82[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2940922	0.89[ASN][1000 genomes]
rs2940923	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2940927	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs2940934	0.91[ASN][1000 genomes]
rs2940940	0.98[ASN][1000 genomes]
rs2940945	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972406	0.91[ASN][1000 genomes]
rs2972407	0.82[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2972408	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2972410	0.89[ASN][1000 genomes]
rs2972411	0.82[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2972412	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2972413	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2972418	0.82[CHB][hapmap]
rs3764453	0.96[ASN][1000 genomes]
rs4358532	0.95[ASN][1000 genomes]
rs4866781	0.89[ASN][1000 genomes]
rs4866782	0.89[ASN][1000 genomes]
rs4866788	0.85[ASN][1000 genomes]
rs4866795	0.94[ASN][1000 genomes]
rs4866896	0.94[ASN][1000 genomes]
rs4866901	0.94[ASN][1000 genomes]
rs4866919	0.89[ASN][1000 genomes]
rs906817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9686537	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9687863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs979233	1.00[ASN][1000 genomes]
rs991592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972394	PCCB	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42388800-42390200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:42390000-42390400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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