Variant report

Variant	rs2423731
Chromosome Location	chr20:13620683-13620684
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr20:13620625-13620950	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13608491..13611413-chr20:13619029..13620797,2	MCF-7	breast:
2	chr20:13620591..13622927-chr20:13625595..13627340,2	K562	blood:

Variant related genes	Relation type
TASP1	TF binding region
ENSG00000089123	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13040087	0.86[AFR][1000 genomes]
rs2070307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295504	0.84[AFR][1000 genomes]
rs2295505	0.95[ASN][1000 genomes]
rs2295506	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2423729	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2423730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2423732	0.85[AFR][1000 genomes]
rs2423734	0.85[AFR][1000 genomes]
rs6033772	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs6033773	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6033778	0.95[ASN][1000 genomes]
rs6033779	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6033783	0.86[AFR][1000 genomes]
rs6042245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6042255	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042256	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042261	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042264	0.81[AFR][1000 genomes]
rs6042266	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6042269	0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042273	0.88[AFR][1000 genomes]
rs6105142	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6109979	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6109983	0.86[AFR][1000 genomes]
rs6109990	0.84[AFR][1000 genomes]
rs6131495	0.95[ASN][1000 genomes]
rs6134937	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs6134938	0.94[CHB][hapmap];0.95[ASN][1000 genomes]
rs6514424	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2423731	TASP1	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13620000-13623200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:13620200-13625000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:13620200-13625400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:13620200-13634800	Weak transcription	Right Atrium	heart
5	chr20:13620400-13621400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:13620400-13625000	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links