Variant report

Variant	rs10494752
Chromosome Location	chr1:197216219-197216220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10801597	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10801598	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10801600	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10801601	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10801602	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10922181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10922190	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10922197	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10922198	0.89[JPT][hapmap];0.92[MEX][hapmap]
rs12022402	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12026252	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045335	0.81[AMR][1000 genomes]
rs1337005	0.82[TSI][hapmap]
rs1337006	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1337007	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1337170	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415210	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1415343	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1577802	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884645	0.81[AMR][1000 genomes]
rs4915393	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915453	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7418217	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7530522	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7547972	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7548481	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553508	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10494752	CFHR5	cis	parietal	SCAN
rs10494752	RGS18	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197213000-197218800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:197215600-197217400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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