Variant report

Variant	rs4668531
Chromosome Location	chr2:7378329-7378330
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1016515	0.85[ASN][1000 genomes]
rs10929471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929472	0.90[ASN][1000 genomes]
rs10929473	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929474	0.97[ASN][1000 genomes]
rs11676725	0.81[ASN][1000 genomes]
rs11680346	0.80[ASN][1000 genomes]
rs11682417	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11687207	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11695715	0.82[ASN][1000 genomes]
rs12612059	0.89[ASN][1000 genomes]
rs12612703	0.82[ASN][1000 genomes]
rs12619070	0.92[ASN][1000 genomes]
rs12621585	0.82[ASN][1000 genomes]
rs12623613	0.82[ASN][1000 genomes]
rs12999068	0.86[ASN][1000 genomes]
rs13002545	0.81[ASN][1000 genomes]
rs13013964	0.97[ASN][1000 genomes]
rs13023691	0.82[ASN][1000 genomes]
rs1404845	0.86[ASN][1000 genomes]
rs1464879	0.81[ASN][1000 genomes]
rs1464880	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1473655	0.89[ASN][1000 genomes]
rs1525490	0.90[ASN][1000 genomes]
rs1525491	0.81[ASN][1000 genomes]
rs1525492	0.92[ASN][1000 genomes]
rs1581562	0.81[ASN][1000 genomes]
rs16866007	0.88[ASN][1000 genomes]
rs16866008	0.88[ASN][1000 genomes]
rs16866010	0.86[ASN][1000 genomes]
rs1880605	0.97[ASN][1000 genomes]
rs1917675	0.81[ASN][1000 genomes]
rs1917676	0.81[ASN][1000 genomes]
rs1917677	0.81[ASN][1000 genomes]
rs1917678	0.86[ASN][1000 genomes]
rs2352713	0.85[ASN][1000 genomes]
rs34130652	0.82[ASN][1000 genomes]
rs34325684	0.86[ASN][1000 genomes]
rs36034588	0.81[ASN][1000 genomes]
rs4233854	0.86[ASN][1000 genomes]
rs4265983	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4356635	0.81[ASN][1000 genomes]
rs4362529	0.81[ASN][1000 genomes]
rs4362530	0.81[ASN][1000 genomes]
rs4669153	0.85[ASN][1000 genomes]
rs4669156	0.86[ASN][1000 genomes]
rs4669158	0.86[ASN][1000 genomes]
rs4669162	0.81[ASN][1000 genomes]
rs4669164	0.90[ASN][1000 genomes]
rs4669169	0.97[ASN][1000 genomes]
rs55869666	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55914055	0.81[ASN][1000 genomes]
rs6738582	0.86[ASN][1000 genomes]
rs6739202	0.81[ASN][1000 genomes]
rs7559257	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs870863	0.81[ASN][1000 genomes]
rs872442	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs960793	0.81[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	nsv915888	chr2:7197783-7461967	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1000136	chr2:7337270-7379211	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	nsv833337	chr2:7337273-7521146	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4668531	HPCAL1	cis	parietal	SCAN
rs4668531	KIDINS220	cis	cerebellum	SCAN
rs4668531	NOL10	cis	parietal	SCAN
rs4668531	LAPTM4B	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7372000-7388400	Weak transcription	Pancreas	Pancrea
2	chr2:7378000-7388400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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