Variant report

Variant	rs12484058
Chromosome Location	chr22:33430898-33430899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11089601	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12484091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894536	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2413161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55851829	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998705	0.81[EUR][1000 genomes]
rs62234240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292646	0.89[ASN][1000 genomes]
rs8138938	0.89[ASN][1000 genomes]
rs9607004	0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607005	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607006	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607007	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs9609679	0.81[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs9609680	0.81[GIH][hapmap]
rs9609681	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs9609683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609684	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609685	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609688	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609690	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609691	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609692	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609693	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609695	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9609696	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12484058	SEC14L3	cis	cerebellum	SCAN
rs12484058	RFPL1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33415000-33434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:33422600-33431000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:33428000-33431000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:33430600-33431200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
5	chr22:33430600-33431200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
6	chr22:33430600-33431600	Enhancers	Liver	Liver
7	chr22:33430600-33432000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr22:33430600-33432200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr22:33430600-33432400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr22:33430600-33432600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr22:33430800-33431000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr22:33430800-33431000	Bivalent Enhancer	Brain Anterior Caudate	brain
13	chr22:33430800-33431200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:33430800-33431800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:33430800-33432200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr22:33430800-33432400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr22:33430800-33432400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr22:33430800-33432600	Enhancers	HUES64 Cell Line	embryonic stem cell

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