Variant report

Variant	rs13074801
Chromosome Location	chr3:143043702-143043703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10804692	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11716489	1.00[JPT][hapmap]
rs11717437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11718728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11927016	1.00[CHB][hapmap]
rs13061014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13099124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1501631	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604377	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1604380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1609727	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610217	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637392	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1812200	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875462	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1995356	1.00[CHB][hapmap]
rs35842913	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839627	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7627844	1.00[CHB][hapmap]
rs7642361	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7652557	1.00[CHB][hapmap]
rs894176	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs9850863	1.00[CHB][hapmap]
rs9862119	1.00[CHB][hapmap]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13074801	PLSCR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143022400-143048200	Weak transcription	Psoas Muscle	Psoas
2	chr3:143026600-143047400	Weak transcription	Spleen	Spleen
3	chr3:143029400-143045800	Weak transcription	Adipose Nuclei	Adipose
4	chr3:143029800-143045200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143033800-143048400	Weak transcription	Fetal Stomach	stomach
6	chr3:143034400-143047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:143034400-143048600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:143037800-143045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:143038200-143045600	Weak transcription	Fetal Lung	lung
10	chr3:143039200-143045200	Weak transcription	Fetal Thymus	thymus
11	chr3:143040400-143045200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:143040800-143045400	Weak transcription	Primary B cells from cord blood	blood
13	chr3:143041400-143045200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:143042800-143043800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:143042800-143043800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:143043400-143048400	Weak transcription	Lung	lung
17	chr3:143043600-143044000	Weak transcription	K562	blood

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