Variant report

Variant	rs6821590
Chromosome Location	chr4:124713216-124713217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10002832	0.93[EUR][1000 genomes]
rs10003021	0.89[EUR][1000 genomes]
rs10028082	0.94[EUR][1000 genomes]
rs10031024	0.93[EUR][1000 genomes]
rs10031632	0.93[EUR][1000 genomes]
rs10031894	0.93[EUR][1000 genomes]
rs10518305	0.80[ASN][1000 genomes]
rs10518306	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11098722	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11729742	0.89[EUR][1000 genomes]
rs1425403	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1425404	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1425406	0.93[EUR][1000 genomes]
rs1425407	0.83[EUR][1000 genomes]
rs1433219	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17007176	1.00[JPT][hapmap]
rs17007241	0.89[EUR][1000 genomes]
rs17007305	0.94[EUR][1000 genomes]
rs17007484	0.80[ASN][1000 genomes]
rs17007499	0.80[ASN][1000 genomes]
rs17007509	0.80[ASN][1000 genomes]
rs17425479	0.80[ASN][1000 genomes]
rs17425951	0.80[ASN][1000 genomes]
rs17491837	0.80[ASN][1000 genomes]
rs1895754	0.89[EUR][1000 genomes]
rs2194866	0.93[EUR][1000 genomes]
rs28361300	0.92[EUR][1000 genomes]
rs28361543	0.94[EUR][1000 genomes]
rs28376823	0.89[EUR][1000 genomes]
rs28470742	0.89[EUR][1000 genomes]
rs28493674	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28595508	0.93[EUR][1000 genomes]
rs28670181	0.94[EUR][1000 genomes]
rs28699481	0.89[EUR][1000 genomes]
rs28805878	0.89[EUR][1000 genomes]
rs4340803	0.80[ASN][1000 genomes]
rs4833290	0.94[EUR][1000 genomes]
rs4833291	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4833292	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4833935	0.89[EUR][1000 genomes]
rs4833939	0.89[EUR][1000 genomes]
rs4833942	0.89[EUR][1000 genomes]
rs4833945	0.81[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4833946	0.94[EUR][1000 genomes]
rs4833947	0.94[EUR][1000 genomes]
rs4833948	0.94[EUR][1000 genomes]
rs4833949	0.93[EUR][1000 genomes]
rs4833952	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57927362	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57978274	0.92[EUR][1000 genomes]
rs58148580	0.80[ASN][1000 genomes]
rs58208464	0.80[ASN][1000 genomes]
rs58498049	0.80[ASN][1000 genomes]
rs58530613	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59468019	0.89[EUR][1000 genomes]
rs6827679	0.94[EUR][1000 genomes]
rs6828406	0.94[EUR][1000 genomes]
rs6847358	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72929724	0.89[EUR][1000 genomes]
rs72929781	0.93[EUR][1000 genomes]
rs7659116	0.93[EUR][1000 genomes]
rs7668462	0.89[EUR][1000 genomes]
rs7677587	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs7691744	0.89[EUR][1000 genomes]
rs7692299	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699549	0.93[EUR][1000 genomes]
rs9631736	0.84[EUR][1000 genomes]
rs9992459	0.94[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	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001751	chr4:124693346-124733305	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6821590	TRPC3	cis	parietal	SCAN
rs6821590	QRFPR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124712400-124713400	Weak transcription	Fetal Muscle Leg	muscle

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