Variant report

Variant	rs358722
Chromosome Location	chr3:155434062-155434063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10936015	0.81[EUR][1000 genomes]
rs117442	0.81[GIH][hapmap]
rs11923772	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs173370	0.81[EUR][1000 genomes]
rs181588	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs184836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2320190	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358714	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358720	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358723	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs358736	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs358738	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358740	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358741	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358744	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358745	0.91[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358746	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs358748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs396797	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs400999	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs426236	0.95[JPT][hapmap]
rs4680215	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4680216	0.95[JPT][hapmap]
rs7619505	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs358722	SLC33A1	cis	parietal	SCAN
rs358722	PLCH1	cis	cerebellum	SCAN
rs358722	SLC33A1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155412600-155437400	Weak transcription	Pancreas	Pancrea
2	chr3:155432400-155434800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:155432400-155461600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:155432600-155434800	Enhancers	HepG2	liver
5	chr3:155432600-155435000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:155432800-155434200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:155432800-155434400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:155433200-155434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:155433200-155435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:155433400-155434200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:155433400-155435200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:155433400-155435200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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