Variant report

Variant	rs2077651
Chromosome Location	chr9:107936434-107936435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10820789	0.85[EUR][1000 genomes]
rs10991567	0.88[ASN][1000 genomes]
rs10991568	0.86[ASN][1000 genomes]
rs10991569	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10991574	0.81[EUR][1000 genomes]
rs11531833	0.84[EUR][1000 genomes]
rs12237108	0.81[EUR][1000 genomes]
rs1979017	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979018	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1979019	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1979020	0.81[ASN][1000 genomes]
rs6479297	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs6479298	0.90[JPT][hapmap]
rs7029699	0.87[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7036983	0.85[EUR][1000 genomes]
rs7038005	0.85[EUR][1000 genomes]
rs7852889	0.84[EUR][1000 genomes]
rs7856908	0.83[EUR][1000 genomes]
rs7858496	0.87[CHB][hapmap];0.90[JPT][hapmap]

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	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2077651	RNF20	cis	parietal	SCAN
rs2077651	OR13F1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:107933000-107936600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:107933200-107937000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr9:107934000-107936800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr9:107934000-107937000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:107934200-107936800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr9:107934200-107937000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:107935200-107936600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:107935200-107937000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:107935200-107937000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr9:107935400-107936800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:107935400-107937000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr9:107935600-107936600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:107935600-107936800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:107935600-107936800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:107935600-107937400	Enhancers	Fetal Lung	lung
16	chr9:107936000-107939800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:107936200-107936600	Enhancers	Fetal Stomach	stomach
18	chr9:107936200-107939800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:107936400-107939000	Weak transcription	Brain Germinal Matrix	brain

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

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