Variant report

Variant	rs1316443
Chromosome Location	chr1:47907662-47907663
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10399673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12070024	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12090153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1680020	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2622909	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622917	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622920	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622921	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2820970	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2820971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2820974	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3738315	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4603175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs505399	0.83[AMR][1000 genomes]
rs524158	0.83[AMR][1000 genomes]
rs527551	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs538286	0.83[AMR][1000 genomes]
rs55718554	0.87[EUR][1000 genomes]
rs557851	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs571281	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61103903	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6673882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6673934	0.85[EUR][1000 genomes]
rs7525184	0.81[GIH][hapmap]
rs7526434	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7552140	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436899	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv2755190	chr1:47907580-48048680	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1316443	CYP4Z2P	cis	parietal	SCAN
rs1316443	CMPK1	cis	parietal	SCAN
rs1316443	CYP4Z2P	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
2	chr1:47904800-47910000	Weak transcription	Pancreas	Pancrea
3	chr1:47905200-47907800	Bivalent/Poised TSS	Fetal Kidney	kidney
4	chr1:47905600-47908600	Active TSS	Colonic Mucosa	Colon
5	chr1:47906000-47910000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr1:47907200-47909000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:47907600-47907800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:47907600-47907800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
9	chr1:47907600-47908000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
10	chr1:47907600-47918400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links