Variant report

Variant	rs12406297
Chromosome Location	chr1:79213655-79213656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10493615	0.83[EUR][1000 genomes]
rs11162539	0.82[EUR][1000 genomes]
rs11162540	0.81[EUR][1000 genomes]
rs11162541	0.81[EUR][1000 genomes]
rs11162544	0.83[EUR][1000 genomes]
rs11587990	0.81[EUR][1000 genomes]
rs12403117	0.82[EUR][1000 genomes]
rs12406475	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409331	0.82[EUR][1000 genomes]
rs12409781	0.82[EUR][1000 genomes]
rs1620302	0.93[ASN][1000 genomes]
rs1625911	0.93[ASN][1000 genomes]
rs1629252	0.93[ASN][1000 genomes]
rs17395034	0.82[EUR][1000 genomes]
rs17395097	0.83[EUR][1000 genomes]
rs17399158	0.83[EUR][1000 genomes]
rs17399192	0.83[EUR][1000 genomes]
rs17399479	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17400419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400647	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400696	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400982	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1887286	0.83[EUR][1000 genomes]
rs1926897	0.82[EUR][1000 genomes]
rs1926898	0.82[EUR][1000 genomes]
rs1926901	0.81[EUR][1000 genomes]
rs1926902	0.82[EUR][1000 genomes]
rs1926903	0.82[EUR][1000 genomes]
rs1926904	0.82[EUR][1000 genomes]
rs1926905	0.82[EUR][1000 genomes]
rs273250	0.84[JPT][hapmap]
rs2767494	0.93[ASN][1000 genomes]
rs58150654	0.82[EUR][1000 genomes]
rs58921479	0.82[EUR][1000 genomes]
rs58945140	0.81[EUR][1000 genomes]
rs58993850	0.82[EUR][1000 genomes]
rs60311076	0.82[EUR][1000 genomes]
rs61613596	0.82[EUR][1000 genomes]
rs61681700	0.82[EUR][1000 genomes]
rs61768666	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770023	0.82[EUR][1000 genomes]
rs61770024	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv871588	chr1:79164901-79214489	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
4	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12406297	IFI44	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79211600-79217200	Weak transcription	Muscle Satellite Cultured Cells	--

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