Variant report

Variant	rs3807390
Chromosome Location	chr7:38573431-38573432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10085389	0.82[JPT][hapmap]
rs1019286	0.82[JPT][hapmap]
rs1019287	0.82[JPT][hapmap]
rs10229905	1.00[JPT][hapmap]
rs10232299	1.00[JPT][hapmap]
rs10245053	1.00[JPT][hapmap]
rs10246472	0.82[JPT][hapmap]
rs10248732	0.82[JPT][hapmap]
rs10249106	0.82[JPT][hapmap]
rs10250342	1.00[JPT][hapmap]
rs10255786	1.00[JPT][hapmap]
rs10259475	1.00[JPT][hapmap]
rs10259950	0.96[ASN][1000 genomes]
rs10264790	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs10265223	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs10266944	1.00[JPT][hapmap]
rs10267691	1.00[JPT][hapmap]
rs10276324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10276544	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs10277878	1.00[JPT][hapmap]
rs10280133	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10280220	1.00[JPT][hapmap]
rs11764380	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2083147	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2267807	1.00[JPT][hapmap]
rs2284248	1.00[JPT][hapmap]
rs3807396	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823595	1.00[JPT][hapmap]
rs4723756	1.00[JPT][hapmap]
rs7777111	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7785965	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7799083	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9638940	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967022	0.96[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	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1018890	chr7:38557432-38600944	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3807390	GLI3	cis	parietal	SCAN
rs3807390	LOC646999	cis	parietal	SCAN
rs3807390	STARD3NL	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38563800-38578400	Weak transcription	Aorta	Aorta
2	chr7:38564200-38580800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:38564800-38578400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:38569600-38574000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:38570400-38575400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:38571000-38574800	Weak transcription	Spleen	Spleen
7	chr7:38572600-38573800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:38573200-38574600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:38573400-38573600	Enhancers	Fetal Heart	heart

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