Variant report

Variant	rs724972
Chromosome Location	chr3:89581408-89581409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11921985	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs11924356	0.97[LWK][hapmap];0.89[YRI][hapmap]
rs12636275	0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520596	0.91[EUR][1000 genomes]
rs2117137	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35124509	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3792572	0.85[CEU][hapmap]
rs6551413	0.91[EUR][1000 genomes]
rs6771054	0.89[CEU][hapmap]
rs6772953	0.85[CEU][hapmap]
rs6795325	0.91[EUR][1000 genomes]
rs73153219	0.91[EUR][1000 genomes]
rs7632427	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7632502	0.81[CEU][hapmap]
rs7637670	0.85[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs7650184	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap]
rs987748	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv590952	chr3:89493167-89727198	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010021	chr3:89521983-90141988	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv524781	chr3:89543677-89597679	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs724972	C3orf38	cis	cerebellum	SCAN
rs724972	EPHA3	cis	cerebellum	SCAN
rs724972	STX19	trans	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89578800-89582400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:89580200-89582000	Weak transcription	Fetal Lung	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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