Variant report

Variant	rs2315942
Chromosome Location	chr3:55855820-55855821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1008	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1495365	0.82[JPT][hapmap]
rs1495366	0.82[JPT][hapmap]
rs1542422	0.94[ASN][1000 genomes]
rs2315944	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4246673	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4459870	0.93[EUR][1000 genomes]
rs4542991	0.85[EUR][1000 genomes]
rs4572738	0.85[EUR][1000 genomes]
rs4592994	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4955882	0.93[EUR][1000 genomes]
rs4955884	0.93[EUR][1000 genomes]
rs4974113	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4974148	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55638022	0.83[AMR][1000 genomes]
rs55665761	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445754	0.84[EUR][1000 genomes]
rs6790618	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796871	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7615473	0.93[EUR][1000 genomes]
rs7616709	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617962	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809248	0.85[EUR][1000 genomes]
rs9815091	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9828807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840522	0.94[EUR][1000 genomes]
rs9860951	0.94[EUR][1000 genomes]
rs9879933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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
rs2315942	HESX1	cis	cerebellum	SCAN
rs2315942	IQCF1	cis	cerebellum	SCAN
rs2315942	CCDC66	cis	parietal	SCAN
rs2315942	RRP9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55847600-55860200	Weak transcription	Fetal Lung	lung

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