Variant report

Variant	rs3092743
Chromosome Location	chr20:41329753-41329754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12479621	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12625206	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987210	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16987212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2206428	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2425515	0.82[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2425536	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3091434	0.83[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[ASN][1000 genomes]
rs3091578	0.90[ASN][1000 genomes]
rs3092078	0.90[ASN][1000 genomes]
rs3092557	0.93[JPT][hapmap]
rs3092592	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3092656	0.87[JPT][hapmap]
rs36020805	0.90[ASN][1000 genomes]
rs41283264	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60275164	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6065520	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs6065522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6065523	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6065524	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6065525	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6072817	0.83[ASN][1000 genomes]
rs6072818	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6072823	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6072824	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6072826	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6072827	0.84[EUR][1000 genomes]
rs6072828	0.83[EUR][1000 genomes]
rs6072829	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6072830	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs62205374	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62205376	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62205381	0.84[ASN][1000 genomes]
rs62205382	0.90[ASN][1000 genomes]
rs73112427	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv532517	chr20:41188651-41342196	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv949644	chr20:41207365-41333541	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912878	chr20:41222480-41361424	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv833988	chr20:41227788-41379921	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv586028	chr20:41296994-41381215	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060878	chr20:41317182-41342290	Weak transcription Strong transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3092743	SPINT4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41327600-41330400	Weak transcription	Liver	Liver
2	chr20:41328600-41330000	Enhancers	Colon Smooth Muscle	Colon
3	chr20:41328600-41330000	Enhancers	Rectal Smooth Muscle	rectum
4	chr20:41328800-41329800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:41329200-41329800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr20:41329400-41330800	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:41329600-41331000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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