Variant report

Variant	rs842199
Chromosome Location	chr12:44457572-44457573
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10736018	0.84[CHB][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs10785492	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs10880608	0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs10880618	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1098878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182382	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12322164	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1688723	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1701083	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701094	0.89[JPT][hapmap]
rs17094183	0.83[CHB][hapmap]
rs2407788	0.85[CHB][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs2657575	0.89[JPT][hapmap]
rs6582496	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7136217	0.88[JPT][hapmap]
rs7312422	0.85[CHB][hapmap];0.87[MKK][hapmap];0.87[ASN][1000 genomes]
rs842193	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs842194	1.00[CEU][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs842195	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs842202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859699	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs863580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs842199	CPNE8	cis	parietal	SCAN
rs842199	ADAMTS20	cis	parietal	SCAN

Chromatin state (count:6 , 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	chr12:44456400-44458200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:44456600-44458600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:44457000-44470600	Weak transcription	Psoas Muscle	Psoas

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