Variant report

Variant	rs56309111
Chromosome Location	chr5:118883824-118883825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10463469	0.85[ASN][1000 genomes]
rs11744058	0.82[ASN][1000 genomes]
rs1298928	0.95[ASN][1000 genomes]
rs17453681	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28943593	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756513	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797371	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56349852	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72788170	0.82[ASN][1000 genomes]
rs73249978	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73249988	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73249999	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73251672	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][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	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882776	chr5:118859546-118915408	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv882777	chr5:118870452-118981480	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56309111	FAM170A	cis	Thyroid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118874800-118890200	Weak transcription	Fetal Heart	heart
2	chr5:118878800-118885600	Weak transcription	Fetal Stomach	stomach
3	chr5:118878800-118886800	Weak transcription	Aorta	Aorta
4	chr5:118878800-118888600	Weak transcription	Ovary	ovary
5	chr5:118879000-118884200	Weak transcription	Lung	lung
6	chr5:118879000-118884600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:118879000-118885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:118879000-118885200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:118879000-118891200	Weak transcription	Pancreas	Pancrea
10	chr5:118879200-118887600	Weak transcription	Adipose Nuclei	Adipose
11	chr5:118879200-118892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:118881400-118890000	Weak transcription	Brain Angular Gyrus	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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