Variant report

Variant	rs4481960
Chromosome Location	chr10:97524313-97524314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10509688	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs10748644	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882658	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882687	0.82[CHB][hapmap]
rs11188426	0.83[ASN][1000 genomes]
rs11188427	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11528095	0.81[ASN][1000 genomes]
rs12414904	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[JPT][hapmap]
rs12768006	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs12773566	1.00[ASW][hapmap];0.83[JPT][hapmap]
rs12783226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1418710	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1933164	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs2861150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3176894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34037152	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35087577	0.84[ASN][1000 genomes]
rs4244321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs483920	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs4918959	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4918963	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4918965	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6584021	0.85[ASN][1000 genomes]
rs67707291	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7090916	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7096610	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72813744	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4481960	SFRP5	cis	cerebellum	SCAN
rs4481960	ENTPD1	cis	lymphoblastoid	seeQTL
rs4481960	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs4481960	GPR120	cis	parietal	SCAN
rs4481960	ZNF518A	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97516800-97524800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:97518600-97534000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:97518800-97534000	Weak transcription	Fetal Stomach	stomach
4	chr10:97520000-97527600	Weak transcription	Small Intestine	intestine
5	chr10:97521800-97527600	Weak transcription	Aorta	Aorta
6	chr10:97521800-97537400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:97521800-97537400	Weak transcription	Lung	lung
8	chr10:97522200-97528000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:97522600-97526400	ZNF genes & repeats	GM12878-XiMat	blood
10	chr10:97523000-97527600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:97523000-97527600	Weak transcription	HUVEC	blood vessel
12	chr10:97523400-97524400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:97523400-97526000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr10:97523800-97524400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr10:97524000-97524600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr10:97524000-97526600	Weak transcription	Primary B cells from cord blood	blood
17	chr10:97524200-97525400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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