Variant report

Variant	rs9860951
Chromosome Location	chr3:55846998-55846999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1008	0.82[EUR][1000 genomes]
rs1495365	0.83[CHB][hapmap]
rs1495366	0.83[CHB][hapmap]
rs2315942	0.94[EUR][1000 genomes]
rs2315944	0.88[EUR][1000 genomes]
rs4246673	0.87[EUR][1000 genomes]
rs4260395	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4459870	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4542991	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4572738	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4592994	0.82[EUR][1000 genomes]
rs4955877	0.82[CHB][hapmap]
rs4955882	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4955884	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974113	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974146	0.85[ASN][1000 genomes]
rs4974147	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974148	0.86[EUR][1000 genomes]
rs55665761	0.84[EUR][1000 genomes]
rs6445754	0.88[EUR][1000 genomes]
rs6790618	0.82[EUR][1000 genomes]
rs6796871	0.81[EUR][1000 genomes]
rs72877116	0.83[ASN][1000 genomes]
rs7615473	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7616709	0.86[EUR][1000 genomes]
rs7617962	0.82[EUR][1000 genomes]
rs7641474	0.80[ASN][1000 genomes]
rs9809248	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815001	0.89[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs9815091	0.81[EUR][1000 genomes]
rs9828807	0.88[EUR][1000 genomes]
rs9835091	0.86[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9838012	0.85[ASN][1000 genomes]
rs9840522	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846380	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9852746	0.89[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9852888	0.89[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9853067	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9854025	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854247	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857120	0.85[ASN][1000 genomes]
rs9866297	0.81[EUR][1000 genomes]
rs9874792	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9879933	0.95[EUR][1000 genomes]

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	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv590361	chr3:55834871-55876104	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9860951	CCDC66	cis	parietal	SCAN
rs9860951	HESX1	cis	cerebellum	SCAN
rs9860951	TWF2	cis	parietal	SCAN
rs9860951	RRP9	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55846000-55847600	Enhancers	Lung	lung
2	chr3:55846400-55848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:55846800-55847000	Bivalent Enhancer	Fetal Lung	lung

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