Variant report

Variant	rs6030670
Chromosome Location	chr20:41775518-41775519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2185591	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2867651	0.84[EUR][1000 genomes]
rs4810375	0.86[GIH][hapmap]
rs4812671	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4812672	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4812681	0.81[YRI][hapmap]
rs6016963	0.80[GIH][hapmap]
rs6030669	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6065581	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6072997	0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6072998	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6103157	0.81[ASN][1000 genomes]
rs870251	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6030670	ANKRD18A	trans	brain	seeQTL
rs6030670	TSPAN8	trans	brain	seeQTL
rs6030670	WFDC10A	cis	cerebellum	SCAN
rs6030670	MAFB	cis	cerebellum	SCAN
rs6030670	PTPRT	cis	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41774000-41775800	Enhancers	Brain Hippocampus Middle	brain
2	chr20:41774400-41775800	Enhancers	Brain Substantia Nigra	brain
3	chr20:41774800-41775600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:41775000-41775800	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:41775200-41775600	Enhancers	Brain Anterior Caudate	brain
6	chr20:41775200-41775600	Enhancers	Fetal Stomach	stomach
7	chr20:41775200-41775800	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr20:41775400-41777200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr20:41775400-41787800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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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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