Variant report

Variant	rs3859549
Chromosome Location	chr19:38306876-38306877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1048505	0.91[ASN][1000 genomes]
rs12150862	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151082	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.91[ASN][1000 genomes]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248097	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17248670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249138	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249336	1.00[CHB][hapmap]
rs17305823	1.00[JPT][hapmap]
rs17306900	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35153242	1.00[JPT][hapmap]
rs4536583	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614853	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55681348	0.86[ASN][1000 genomes]
rs55743020	0.91[ASN][1000 genomes]
rs55752822	0.81[EUR][1000 genomes]
rs55813548	0.81[EUR][1000 genomes]
rs55974157	0.81[EUR][1000 genomes]
rs55983118	0.81[EUR][1000 genomes]
rs56184201	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207124	0.81[EUR][1000 genomes]
rs56230664	0.81[EUR][1000 genomes]
rs56233644	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246446	0.81[EUR][1000 genomes]
rs56268127	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290614	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351266	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.81[EUR][1000 genomes]
rs6508755	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs705501	1.00[CHB][hapmap]
rs7245855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73027472	0.84[EUR][1000 genomes]
rs73027480	0.84[EUR][1000 genomes]
rs73039029	0.91[ASN][1000 genomes]
rs73041006	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73041036	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343065	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs8100199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8110293	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3859549	AC012309.5	cis	Esophagus Muscularis	GTEx
rs3859549	AC012309.5	cis	Esophagus Mucosa	GTEx
rs3859549	ZNF781	cis	Thyroid	GTEx
rs3859549	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs3859549	AC012309.5	cis	Thyroid	GTEx
rs3859549	AC012309.5	cis	Heart Left Ventricle	GTEx
rs3859549	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38304200-38307400	Weak transcription	Ovary	ovary
2	chr19:38304200-38307600	Weak transcription	Aorta	Aorta
3	chr19:38306200-38307600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:38306800-38307200	Weak transcription	Colon Smooth Muscle	Colon

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