Variant report

Variant	rs1398440
Chromosome Location	chr12:85790809-85790810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10746344	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10746346	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746347	0.88[ASN][1000 genomes]
rs10779161	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779164	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779167	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779168	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779169	0.89[ASN][1000 genomes]
rs10779170	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10779173	0.88[ASN][1000 genomes]
rs10862979	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862990	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10862991	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10862993	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10862999	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863000	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863007	0.88[ASN][1000 genomes]
rs10863008	0.88[ASN][1000 genomes]
rs11116807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116832	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11116833	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11116930	0.86[ASN][1000 genomes]
rs11116934	0.82[ASN][1000 genomes]
rs11116935	0.82[ASN][1000 genomes]
rs11831266	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12578708	0.83[ASN][1000 genomes]
rs1398442	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1870933	0.87[ASN][1000 genomes]
rs1870935	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2199513	0.83[ASN][1000 genomes]
rs2199516	0.88[ASN][1000 genomes]
rs2199517	0.88[ASN][1000 genomes]
rs2199518	0.88[ASN][1000 genomes]
rs2405248	0.87[ASN][1000 genomes]
rs2405254	0.83[ASN][1000 genomes]
rs4761063	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6419420	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6419421	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539899	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6539901	0.81[ASN][1000 genomes]
rs7133855	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134486	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136236	0.86[ASN][1000 genomes]
rs7297262	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303316	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7316167	0.83[ASN][1000 genomes]
rs7485084	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7485590	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7486767	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7487599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957797	0.97[ASN][1000 genomes]
rs7973323	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7977259	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898986	0.86[ASN][1000 genomes]
rs9788015	0.88[ASN][1000 genomes]
rs9788074	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv899393	chr12:85674707-85796968	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv899394	chr12:85702371-85796968	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1052513	chr12:85721058-85799332	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1398440	NTS	cis	lymphoblastoid	seeQTL
rs1398440	RASSF9	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85787800-85791800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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