Variant report

Variant	rs717372
Chromosome Location	chr9:17699981-17699982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10756899	1.00[CHB][hapmap]
rs10756901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10756902	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs10756904	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap]
rs10756906	0.83[EUR][1000 genomes]
rs10756907	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10756908	0.83[EUR][1000 genomes]
rs10810829	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10810830	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810834	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[TSI][hapmap]
rs10810848	1.00[LWK][hapmap]
rs10963233	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[TSI][hapmap]
rs11789626	1.00[LWK][hapmap]
rs1536072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs1536076	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs2209440	0.95[CHB][hapmap]
rs3808734	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892674	chr9:17631186-17699981	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv1016971	chr9:17648242-17720176	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv1021022	chr9:17649360-17723730	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv892675	chr9:17694823-17790526	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv466279	chr9:17699981-17726581	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv613705	chr9:17699981-17726581	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs717372	SH3GL2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17699400-17700600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:17699400-17700600	Enhancers	Fetal Brain Male	brain
3	chr9:17699800-17700600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:17699800-17701400	Enhancers	Pancreatic Islets	Pancreatic Islet

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Input of quick search could be:

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

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