Variant report

Variant	rs1450519
Chromosome Location	chr3:161094930-161094931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161041944..161044676-chr3:161093934..161096630,2	MCF-7	breast:
2	chr3:161093470..161095509-chr8:98607187..98608759,2	MCF-7	breast:
3	chr17:48942183..48944855-chr3:161092802..161095476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229980	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000240138	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10513564	0.81[CEU][hapmap]
rs10936227	1.00[CEU][hapmap];0.86[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11711695	0.80[CEU][hapmap]
rs11715591	0.81[CEU][hapmap]
rs11718905	0.80[CEU][hapmap]
rs12488878	0.94[CHB][hapmap]
rs13059340	0.81[CEU][hapmap]
rs13073147	0.81[CEU][hapmap]
rs13084731	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13084746	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1382429	0.81[CEU][hapmap]
rs1450521	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1450522	0.81[CEU][hapmap]
rs1450523	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1471440	0.83[CHB][hapmap]
rs163138	0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs16832082	0.81[CEU][hapmap]
rs2054710	0.81[CEU][hapmap]
rs2122527	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs336544	0.83[CHB][hapmap]
rs336545	0.83[CHB][hapmap]
rs336546	0.83[CHB][hapmap]
rs336564	0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs336565	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs336566	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs336571	0.83[ASN][1000 genomes]
rs336573	0.82[ASN][1000 genomes]
rs336574	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs336576	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs336581	0.84[ASN][1000 genomes]
rs336584	0.84[ASN][1000 genomes]
rs336587	0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs336588	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs336592	0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs419703	0.84[ASN][1000 genomes]
rs4487256	0.83[CHB][hapmap]
rs455739	0.86[ASN][1000 genomes]
rs458197	0.85[ASN][1000 genomes]
rs459067	0.85[ASN][1000 genomes]
rs461616	0.86[ASN][1000 genomes]
rs462081	0.86[ASN][1000 genomes]
rs4856701	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4856703	0.81[CEU][hapmap]
rs4856769	0.81[CEU][hapmap]
rs60625846	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441374	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6780536	0.81[CEU][hapmap]
rs67988738	0.84[EUR][1000 genomes]
rs6799805	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs7610800	0.81[CEU][hapmap]
rs7622060	0.94[CHB][hapmap]
rs978933	0.83[CHB][hapmap]
rs9811833	0.83[CHB][hapmap]
rs9812083	0.83[CHB][hapmap]
rs9827833	0.83[CHB][hapmap]
rs9828189	0.83[CHB][hapmap]
rs9828231	0.82[CHB][hapmap]
rs9839404	0.83[CHB][hapmap]
rs9844862	0.88[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1450519	NMD3	cis	parietal	SCAN
rs1450519	C3orf57	cis	parietal	SCAN
rs1450519	SPTSSB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161091200-161096800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:161091400-161102800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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