Variant report

Variant	rs2423761
Chromosome Location	chr20:13905048-13905049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13039593	1.00[LWK][hapmap]
rs1980566	1.00[EUR][1000 genomes]
rs2180226	1.00[EUR][1000 genomes]
rs2258091	1.00[EUR][1000 genomes]
rs2423756	1.00[EUR][1000 genomes]
rs243909	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs243910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs243911	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs243912	1.00[EUR][1000 genomes]
rs243914	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs378135	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4239711	1.00[EUR][1000 genomes]
rs4239712	1.00[EUR][1000 genomes]
rs6033853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033856	1.00[EUR][1000 genomes]
rs6042426	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6042480	1.00[LWK][hapmap]
rs6105192	1.00[EUR][1000 genomes]
rs6131538	1.00[EUR][1000 genomes]
rs660710	1.00[EUR][1000 genomes]
rs761811	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv585437	chr20:13894869-13938789	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2423761	SCT	trans	lymphoblastoid	seeQTL
rs2423761	SNRNP35	trans	lymphoblastoid	seeQTL
rs2423761	CSTA	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13894400-13907000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:13901800-13906600	Weak transcription	Fetal Brain Male	brain
3	chr20:13903400-13907000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:13903800-13907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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