Variant report

Variant	rs1565620
Chromosome Location	chr12:44459583-44459584
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10785492	0.89[CEU][hapmap]
rs10880608	0.89[CEU][hapmap]
rs10880616	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880617	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880618	1.00[JPT][hapmap]
rs11182344	1.00[CHD][hapmap]
rs11182360	1.00[CHB][hapmap]
rs11182369	1.00[CHB][hapmap]
rs11182373	1.00[CHB][hapmap]
rs11182375	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182378	1.00[CHB][hapmap]
rs11182381	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11182384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182387	1.00[CHB][hapmap]
rs11182390	1.00[CHB][hapmap]
rs11182391	1.00[CHB][hapmap]
rs11182396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11182399	1.00[CHB][hapmap]
rs11182402	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182404	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228693	1.00[CHB][hapmap]
rs12230287	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231403	1.00[CHB][hapmap]
rs12296857	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12301507	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12313365	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1701083	1.00[JPT][hapmap]
rs17093973	0.89[TSI][hapmap]
rs17094007	0.82[MEX][hapmap];0.94[TSI][hapmap]
rs17094013	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1976211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407788	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs2407789	0.84[TSI][hapmap]
rs3929354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55756710	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198335	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56227915	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56337317	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6582494	0.91[AMR][1000 genomes]
rs6582495	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7136217	0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7303909	0.82[MEX][hapmap];0.89[TSI][hapmap]
rs73087684	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73087700	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089723	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091745	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7312422	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs7959226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980005	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs842194	1.00[JPT][hapmap]
rs9919676	1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919742	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832390	chr12:44318071-44512114	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1041188	chr12:44331098-44528712	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832391	chr12:44394137-44552555	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44439200-44464400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:44447000-44459800	Weak transcription	Gastric	stomach
3	chr12:44454000-44470400	Weak transcription	Fetal Brain Female	brain
4	chr12:44457000-44470600	Weak transcription	Psoas Muscle	Psoas
5	chr12:44458200-44466000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:44458400-44482200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:44459400-44460200	Enhancers	Pancreatic Islets	Pancreatic Islet

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