Variant report

Variant	rs7798431
Chromosome Location	chr7:25860812-25860813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10225976	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10232819	0.97[EUR][1000 genomes]
rs10238703	0.90[ASN][1000 genomes]
rs10241634	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10241659	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10242536	0.90[ASN][1000 genomes]
rs10245353	0.83[ASN][1000 genomes]
rs10260677	0.89[ASN][1000 genomes]
rs10261019	0.97[EUR][1000 genomes]
rs10262483	0.90[ASN][1000 genomes]
rs10267498	0.90[ASN][1000 genomes]
rs10271088	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271460	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10274306	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282436	0.89[ASN][1000 genomes]
rs1055144	0.89[ASN][1000 genomes]
rs11770186	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs11976790	0.92[EUR][1000 genomes]
rs12535837	0.99[EUR][1000 genomes]
rs12666961	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12700667	0.85[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1376527	0.97[EUR][1000 genomes]
rs1451382	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451383	0.91[EUR][1000 genomes]
rs1451385	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2060765	0.89[EUR][1000 genomes]
rs2391168	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28473292	0.90[ASN][1000 genomes]
rs28858973	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2893220	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2893221	0.91[ASN][1000 genomes]
rs35766302	0.90[ASN][1000 genomes]
rs3902751	0.99[EUR][1000 genomes]
rs4141278	0.84[ASN][1000 genomes]
rs41469349	0.89[ASN][1000 genomes]
rs4722526	0.99[EUR][1000 genomes]
rs4722527	0.99[EUR][1000 genomes]
rs4722528	0.97[EUR][1000 genomes]
rs4722529	0.95[EUR][1000 genomes]
rs4722531	0.94[EUR][1000 genomes]
rs56376645	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57246313	0.86[ASN][1000 genomes]
rs60643312	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61140461	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62447896	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6461887	0.96[EUR][1000 genomes]
rs6958350	0.97[EUR][1000 genomes]
rs7782246	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7782292	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7793216	0.92[EUR][1000 genomes]
rs7798002	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7798130	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs979165	0.96[EUR][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
rs7798431	SKAP2	cis	cerebellum	SCAN
rs7798431	CCDC126	cis	parietal	SCAN

Chromatin state (count:5 , 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

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