Variant report

Variant	rs3739992
Chromosome Location	chr10:38091148-38091149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10508861	0.90[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11011371	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1208619	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1208621	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12243792	0.90[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12265979	0.90[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs12412402	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12413854	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16937571	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1735625	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs176460	0.82[ASN][1000 genomes]
rs1779073	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs200907	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs200909	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs200913	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs200914	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200941	0.81[EUR][1000 genomes]
rs200944	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2738221	0.83[EUR][1000 genomes]
rs2753883	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55738335	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55742761	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59486180	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67276704	0.85[EUR][1000 genomes]
rs68087889	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7068885	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs766362	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7895468	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7912428	0.82[ASN][1000 genomes]
rs9787493	0.82[ASN][1000 genomes]

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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3739992	ZNF25	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38081200-38092000	Weak transcription	Ovary	ovary
2	chr10:38081200-38092200	Weak transcription	Pancreas	Pancrea
3	chr10:38081200-38097200	Weak transcription	Aorta	Aorta
4	chr10:38084400-38092200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:38085400-38100800	Weak transcription	Left Ventricle	heart
6	chr10:38086000-38091800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:38087400-38094600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:38087600-38091200	Weak transcription	HSMMtube	muscle
9	chr10:38088000-38092800	Weak transcription	Brain Hippocampus Middle	brain
10	chr10:38088600-38091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:38088800-38091200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:38090000-38093200	Weak transcription	Brain Substantia Nigra	brain
13	chr10:38090400-38101000	Weak transcription	HepG2	liver
14	chr10:38090600-38091200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:38090600-38091400	ZNF genes & repeats	Liver	Liver
16	chr10:38090600-38093000	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:38090800-38092200	Weak transcription	Adipose Nuclei	Adipose
18	chr10:38090800-38102200	Weak transcription	Brain Angular Gyrus	brain

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