Variant report

Variant	rs1930137
Chromosome Location	chr9:101322370-101322371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1167767	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs2184026	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2259639	0.89[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2778901	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2779521	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2779605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808521	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs2808524	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2808525	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808526	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2808527	0.88[EUR][1000 genomes]
rs2808569	0.87[ASN][1000 genomes]
rs944686	0.89[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs944687	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv6633	chr9:101308371-101342811	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1930137	RNF20	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101314400-101326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:101320400-101322400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:101320400-101322600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:101320800-101322400	Enhancers	Liver	Liver
5	chr9:101321800-101322400	Enhancers	Brain Hippocampus Middle	brain
6	chr9:101321800-101322800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

Quick Search:

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

what's new

Quick links