Variant report

Variant	rs643975
Chromosome Location	chr6:142844251-142844252
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484733	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11155242	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11759653	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12189838	0.85[EUR][1000 genomes]
rs12190271	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12197866	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12213892	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13198644	0.84[EUR][1000 genomes]
rs1329705	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17071756	0.85[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs171891	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928528	0.84[EUR][1000 genomes]
rs2294775	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs262117	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs262118	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262130	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817928	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4304190	0.84[EUR][1000 genomes]
rs6570511	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6900087	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6900233	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6901807	0.85[EUR][1000 genomes]
rs6903424	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6906468	0.85[EUR][1000 genomes]
rs6912639	0.85[EUR][1000 genomes]
rs6922607	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6925979	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7756434	0.85[EUR][1000 genomes]
rs7757571	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7765770	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7776356	0.84[EUR][1000 genomes]
rs9373347	0.84[EUR][1000 genomes]
rs9403386	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs984932	0.83[AFR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs643975	SF3B5	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142840600-142846800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:142843200-142846000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:142843400-142844600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:142843400-142846000	Enhancers	Fetal Lung	lung
5	chr6:142843600-142845200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:142844000-142844400	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr6:142844000-142845400	Enhancers	Brain Germinal Matrix	brain
8	chr6:142844200-142845000	Weak transcription	Fetal Stomach	stomach
9	chr6:142844200-142845000	Enhancers	Stomach Smooth Muscle	stomach
10	chr6:142844200-142845200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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