Variant report

Variant	rs1122452
Chromosome Location	chr3:143427340-143427341
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143424621..143427520-chr3:143427541..143429252,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1124328	0.93[ASW][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs1124329	0.93[ASW][hapmap];0.88[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs11919382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233450	0.82[ASN][1000 genomes]
rs12493345	0.80[ASN][1000 genomes]
rs1562495	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1597081	0.81[CHB][hapmap]
rs1900647	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1900648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2801	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240552	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4839655	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56126118	0.80[ASN][1000 genomes]
rs56231817	0.80[ASN][1000 genomes]
rs6440184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440185	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782663	0.80[CHB][hapmap]
rs7625330	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765723	0.88[YRI][hapmap]
rs9828519	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9835877	0.93[CHB][hapmap]
rs9836173	0.82[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	esv3411176	chr3:143423880-143457059	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1012559	chr3:143424787-143444900	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1122452	PLSCR1	cis	parietal	SCAN
rs1122452	HPS3	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143394200-143470200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:143418000-143431200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:143418800-143428600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:143419200-143428400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:143425400-143427600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:143426400-143427400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:143426600-143427400	Enhancers	HSMMtube	muscle
8	chr3:143426800-143427400	Enhancers	Esophagus	oesophagus
9	chr3:143426800-143427400	Enhancers	Psoas Muscle	Psoas
10	chr3:143427000-143428400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:143427200-143427400	Enhancers	Brain Substantia Nigra	brain
12	chr3:143427200-143428200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:143427200-143429600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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