Variant report

Variant	rs6138150
Chromosome Location	chr20:23847009-23847010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11698737	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11698834	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11699452	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11699520	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071444	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34269359	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35138163	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35275385	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35557175	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35722487	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4322904	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4642010	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6036561	0.87[EUR][1000 genomes]
rs6049191	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049196	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049197	0.87[EUR][1000 genomes]
rs6132673	0.83[EUR][1000 genomes]
rs6132677	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6132679	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138130	0.82[EUR][1000 genomes]
rs6138131	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138148	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6138149	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6138151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6138152	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6138153	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6515431	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6515432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66754062	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67121560	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8182947	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs8184710	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv912823	chr20:23756139-23847009	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv3336	chr20:23804081-23848943	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv585730	chr20:23809681-23862844	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3342719	chr20:23846789-23847230	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to TNF antagonist treatment	18615156	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138150	CST1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23841200-23847600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:23841400-23847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:23847000-23847200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:23847000-23847200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:23847000-23847800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23847000-23848200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr20:23847000-23848200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:23847000-23848400	Enhancers	Fetal Thymus	thymus
9	chr20:23847000-23848800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr20:23847000-23848800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr20:23847000-23849200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr20:23847000-23852400	Enhancers	H1 Cell Line	embryonic stem cell

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