Variant report

Variant	rs16831291
Chromosome Location	chr3:179968336-179968337
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	chr3:179962130..179964163-chr3:179967255..179968786,2	MCF-7	breast:
2	chr3:179966877..179968813-chr3:179972881..179975215,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10222375	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937025	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11705819	0.89[CEU][hapmap]
rs11711435	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919997	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921001	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928576	0.89[CEU][hapmap]
rs11929432	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1525275	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831208	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16831374	0.89[EUR][1000 genomes]
rs16831394	0.82[EUR][1000 genomes]
rs17695226	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28828972	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849422	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3849423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065312	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065331	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73065342	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065358	0.89[EUR][1000 genomes]
rs7647413	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817362	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817801	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822150	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869409	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9870444	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875212	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16831291	LYPD5	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179967200-179970000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179967400-179972200	Enhancers	HMEC	breast

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