Variant report

Variant	rs17110984
Chromosome Location	chr10:97332195-97332196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10509689	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882639	1.00[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs11188385	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11188395	0.82[EUR][1000 genomes]
rs11188402	0.80[EUR][1000 genomes]
rs11188434	1.00[JPT][hapmap]
rs12098522	0.91[JPT][hapmap]
rs17110981	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110999	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933168	0.90[JPT][hapmap]
rs3829157	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs56055942	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56085433	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56193579	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584020	0.90[JPT][hapmap]
rs7072291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7076303	0.81[EUR][1000 genomes]
rs7089081	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73327043	0.81[EUR][1000 genomes]
rs73327044	0.81[EUR][1000 genomes]
rs74150942	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7895441	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7895976	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7897091	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7899286	0.85[TSI][hapmap]
rs7906450	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7908923	0.80[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17110984	PDE6C	cis	cerebellum	SCAN
rs17110984	ZFYVE27	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97321600-97332200	Weak transcription	Right Ventricle	heart
2	chr10:97321800-97332200	Weak transcription	Brain Anterior Caudate	brain
3	chr10:97328800-97332200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr10:97330600-97332600	Enhancers	Ovary	ovary
5	chr10:97330800-97332400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:97331800-97332200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr10:97332000-97332200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:97332000-97332200	Enhancers	Brain Cingulate Gyrus	brain
9	chr10:97332000-97332200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
10	chr10:97332000-97332200	Enhancers	Fetal Lung	lung
11	chr10:97332000-97332400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:97332000-97332400	Enhancers	Colon Smooth Muscle	Colon
13	chr10:97332000-97332600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:97332000-97332600	Enhancers	Adipose Nuclei	Adipose
15	chr10:97332000-97332600	Enhancers	Fetal Muscle Leg	muscle
16	chr10:97332000-97332600	Enhancers	Fetal Stomach	stomach
17	chr10:97332000-97332600	Enhancers	Psoas Muscle	Psoas
18	chr10:97332000-97332600	Active TSS	Right Atrium	heart
19	chr10:97332000-97332600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr10:97332000-97332600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr10:97332000-97333600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr10:97332000-97334200	Enhancers	HSMMtube	muscle

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