Variant report

Variant	rs12535837
Chromosome Location	chr7:25861138-25861139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10225976	0.97[EUR][1000 genomes]
rs10232819	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10241659	0.99[EUR][1000 genomes]
rs10261019	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10271088	0.98[EUR][1000 genomes]
rs10271460	0.99[EUR][1000 genomes]
rs10274306	0.99[EUR][1000 genomes]
rs11770186	0.83[CEU][hapmap]
rs11976790	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666961	0.83[CEU][hapmap]
rs12700667	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1376527	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1451382	0.99[EUR][1000 genomes]
rs1451383	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1451385	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1812673	0.82[ASN][1000 genomes]
rs2060765	0.89[EUR][1000 genomes]
rs2893220	0.99[EUR][1000 genomes]
rs3902751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722526	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722527	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722528	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4722529	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4722531	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56376645	0.94[EUR][1000 genomes]
rs60643312	0.97[EUR][1000 genomes]
rs61140461	0.99[EUR][1000 genomes]
rs62447896	0.99[EUR][1000 genomes]
rs6461887	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6958350	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7782246	0.98[EUR][1000 genomes]
rs7782292	0.99[EUR][1000 genomes]
rs7793216	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7798431	0.99[EUR][1000 genomes]
rs979165	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12535837	SKAP2	cis	cerebellum	SCAN
rs12535837	CCDC126	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25844200-25869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:25847800-25869000	Weak transcription	Psoas Muscle	Psoas
3	chr7:25860800-25861200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:25860800-25861200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:25860800-25861600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:25861000-25861400	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links