Variant report

Variant	rs10039203
Chromosome Location	chr5:178334673-178334674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10035741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10037614	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10039702	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10041805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10043597	0.87[EUR][1000 genomes]
rs10059618	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059708	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10068330	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10068408	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10074505	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10223205	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11739705	0.80[CHB][hapmap]
rs12657785	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1963050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2411991	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61747996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600995	0.83[YRI][hapmap]
rs6874421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6877197	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6896077	0.82[ASN][1000 genomes]
rs72814700	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72814702	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72816603	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72816608	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72816609	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72816613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72816625	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72816629	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72816634	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7725272	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3470830	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3470831	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10039203	ZNF454	cis	Skin Sun Exposed Lower leg	GTEx
rs10039203	ZNF454	cis	parietal	SCAN
rs10039203	ZNF354B	cis	cerebellum	SCAN
rs10039203	FAF2	cis	parietal	SCAN
rs10039203	OR2V2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178323600-178335400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:178323800-178336200	Weak transcription	Right Ventricle	heart
3	chr5:178323800-178336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:178333000-178335800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:178333400-178335600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:178333400-178335600	Weak transcription	Brain Substantia Nigra	brain
7	chr5:178333400-178335600	Weak transcription	Left Ventricle	heart
8	chr5:178333400-178335800	Weak transcription	Gastric	stomach
9	chr5:178333400-178336000	Weak transcription	Brain Angular Gyrus	brain
10	chr5:178333400-178336200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:178333400-178336200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:178333400-178336200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:178334200-178334800	Strong transcription	Ovary	ovary

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