Variant report

Variant	rs13016456
Chromosome Location	chr2:213240319-213240320
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10165393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176489	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs10186360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186462	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205953	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10211056	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs10497971	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11682488	0.91[EUR][1000 genomes]
rs12104818	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12104831	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12694278	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12994366	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12994616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13004266	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13014726	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs13015805	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs13016554	0.83[EUR][1000 genomes]
rs13027907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13030181	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13034566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13034755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394800	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1505351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1505352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1505375	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848535	1.00[JPT][hapmap]
rs16848540	1.00[JPT][hapmap]
rs1876047	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2013073	0.94[EUR][1000 genomes]
rs28510380	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34416516	0.85[ASN][1000 genomes]
rs34623832	0.83[EUR][1000 genomes]
rs34777887	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508685	0.95[ASN][1000 genomes]
rs35880620	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4627509	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs62184103	0.82[EUR][1000 genomes]
rs6738011	1.00[JPT][hapmap]
rs73987402	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv834527	chr2:213115966-213334308	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014680	chr2:213142147-213301614	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv875811	chr2:213200920-213347104	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv3149	chr2:213204282-213248966	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv584422	chr2:213214303-213270427	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1003694	chr2:213216431-213290523	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13016456	RPE	cis	cerebellum	SCAN
rs13016456	PTH2R	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213237800-213241000	Weak transcription	Brain Substantia Nigra	brain
2	chr2:213240200-213240400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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