Variant report

Variant	rs1402223
Chromosome Location	chr3:180049954-180049955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10513774	0.96[ASN][1000 genomes]
rs10937031	1.00[ASN][1000 genomes]
rs10937032	0.97[ASN][1000 genomes]
rs10937034	0.88[ASN][1000 genomes]
rs11707003	0.99[ASN][1000 genomes]
rs12054337	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493613	0.86[CHB][hapmap]
rs12630277	0.99[ASN][1000 genomes]
rs12635401	1.00[ASN][1000 genomes]
rs12635502	0.97[ASN][1000 genomes]
rs12636512	0.97[ASN][1000 genomes]
rs13325203	1.00[ASN][1000 genomes]
rs1356909	1.00[ASN][1000 genomes]
rs1402219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402220	0.92[ASN][1000 genomes]
rs1402224	0.96[ASN][1000 genomes]
rs1402225	0.99[ASN][1000 genomes]
rs1402226	0.97[ASN][1000 genomes]
rs1402227	0.96[ASN][1000 genomes]
rs1402229	0.97[ASN][1000 genomes]
rs1402230	0.97[ASN][1000 genomes]
rs1464359	0.96[ASN][1000 genomes]
rs1464360	0.96[ASN][1000 genomes]
rs16831509	0.97[ASN][1000 genomes]
rs2203980	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28823929	0.97[ASN][1000 genomes]
rs34626513	0.91[ASN][1000 genomes]
rs4306858	0.95[ASN][1000 genomes]
rs4519699	0.96[ASN][1000 genomes]
rs4553975	0.97[ASN][1000 genomes]
rs4572765	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4854908	1.00[ASN][1000 genomes]
rs4854971	1.00[ASN][1000 genomes]
rs4854972	0.97[ASN][1000 genomes]
rs4854973	0.99[ASN][1000 genomes]
rs4854974	0.96[ASN][1000 genomes]
rs61377300	0.94[ASN][1000 genomes]
rs62290971	1.00[ASN][1000 genomes]
rs62290972	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290975	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290976	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62292329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62292330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768614	0.97[ASN][1000 genomes]
rs6785130	0.97[ASN][1000 genomes]
rs6789456	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6797893	0.97[ASN][1000 genomes]
rs7431270	0.95[ASN][1000 genomes]
rs7646778	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646787	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939442	0.82[MEX][hapmap];0.82[MKK][hapmap]
rs950364	0.97[ASN][1000 genomes]
rs9637447	1.00[ASN][1000 genomes]
rs9637455	1.00[ASN][1000 genomes]
rs9713891	0.88[EUR][1000 genomes]
rs9810983	0.99[ASN][1000 genomes]
rs9816991	0.96[ASN][1000 genomes]
rs9857022	0.89[ASN][1000 genomes]
rs9871421	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402223	LAMP3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180047200-180052800	Weak transcription	Ovary	ovary
2	chr3:180049800-180050000	Enhancers	GM12878-XiMat	blood
3	chr3:180049800-180061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links