Variant report

Variant	rs358902
Chromosome Location	chr3:155403530-155403531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155285221..155287488-chr3:155402814..155405461,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1005736	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10936013	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12486000	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12488087	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12490748	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12493067	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs13076587	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13079863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082287	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs13084995	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13087389	0.87[ASN][1000 genomes]
rs13089059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1519532	0.81[JPT][hapmap]
rs1519533	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1519534	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1519535	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs168601	0.85[JPT][hapmap]
rs173384	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1835212	0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1879090	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879092	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2203886	0.91[ASN][1000 genomes]
rs2222275	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2435194	0.82[JPT][hapmap]
rs34810038	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs358704	0.91[JPT][hapmap]
rs358706	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358707	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358708	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358710	0.81[JPT][hapmap]
rs358711	0.81[JPT][hapmap]
rs358712	0.82[JPT][hapmap]
rs358727	0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358732	0.83[MEX][hapmap]
rs358734	0.83[MEX][hapmap]
rs358896	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358898	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358903	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap]
rs358904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358910	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358911	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs358912	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs359541	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs359543	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs359545	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs359546	0.86[JPT][hapmap]
rs359560	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs359567	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs378905	0.82[JPT][hapmap]
rs386867	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392521	0.82[JPT][hapmap]
rs394419	0.82[JPT][hapmap]
rs4083041	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs412664	0.84[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs417877	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426069	0.81[ASN][1000 genomes]
rs430008	0.82[JPT][hapmap]
rs446716	0.82[JPT][hapmap]
rs448062	0.82[JPT][hapmap]
rs4679748	0.81[JPT][hapmap]
rs498378	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs592982	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs597718	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs629698	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs6441000	0.81[JPT][hapmap]
rs6441006	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67428377	0.83[AMR][1000 genomes]
rs6772682	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6777741	0.90[JPT][hapmap]
rs67955071	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808257	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs687462	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7428196	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7645831	0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs358902	SLC33A1	cis	parietal	SCAN
rs358902	SLC33A1	cis	cerebellum	SCAN
rs358902	PLCH1	cis	cerebellum	SCAN
rs358902	SMC4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155395200-155412000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:155400600-155404000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:155400600-155408800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
7	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:155401000-155408800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:155402600-155404600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:155403400-155403600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links