Variant report

Variant	rs6065582
Chromosome Location	chr20:41771701-41771702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1539036	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1572925	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1572926	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs2867651	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4812672	0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6065578	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6065579	0.85[CHB][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs6072990	0.84[MEX][hapmap]
rs6130299	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs947204	0.90[CHB][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs947206	0.84[CHB][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2751914	chr20:41744586-41890453	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6065582	SPINT3	cis	parietal	SCAN
rs6065582	C20orf165	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41767200-41775000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr20:41767600-41772400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:41769200-41774400	Weak transcription	Brain Substantia Nigra	brain
4	chr20:41769400-41774000	Weak transcription	Brain Hippocampus Middle	brain
5	chr20:41770000-41774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:41770200-41774800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:41771400-41772800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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