Variant report

Variant	rs9871574
Chromosome Location	chr3:159098996-159098997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1122205	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11921343	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1349165	0.93[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs1349166	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs1449018	0.93[CEU][hapmap];0.92[JPT][hapmap]
rs1449019	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs1449025	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1530726	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562669	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1823311	0.85[CEU][hapmap]
rs1868415	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2365820	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2365821	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs35886259	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4440163	0.93[CEU][hapmap]
rs6441254	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6771767	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777541	0.86[CEU][hapmap]
rs6780514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6807305	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6810169	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720397	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs7611870	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7629577	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7629583	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7630467	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs7640445	0.86[CEU][hapmap]
rs7651493	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283611	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9290036	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9290039	0.86[CEU][hapmap]
rs9290041	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9290042	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9681445	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9809459	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9823822	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9825664	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9832614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834337	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9855118	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9865361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs9867432	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9873091	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9874504	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9874862	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1004990	chr3:159090974-159174954	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9871574	C3orf55	cis	cerebellum	SCAN
rs9871574	VEPH1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159098600-159099600	Enhancers	Colon Smooth Muscle	Colon

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