Variant report

Variant	rs1799841
Chromosome Location	chr20:23860178-23860179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2071442	0.88[YRI][hapmap]
rs2071443	0.86[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2071445	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2285059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4239744	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4813509	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4815244	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6036565	0.90[EUR][1000 genomes]
rs6076157	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv964382	chr20:23856148-23862860	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	esv3432957	chr20:23858584-23901200	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1799841	CST5	cis	lung	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23848800-23860400	Enhancers	Fetal Thymus	thymus
2	chr20:23852400-23864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:23854800-23860600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr20:23857400-23860600	Weak transcription	Colon Smooth Muscle	Colon
5	chr20:23858200-23862800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:23859200-23861800	Enhancers	Lung	lung
7	chr20:23859400-23860800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:23859400-23861400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr20:23859400-23862400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:23859600-23860200	Active TSS	Spleen	Spleen
11	chr20:23859600-23860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:23859600-23860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr20:23859600-23860600	Weak transcription	HMEC	breast
14	chr20:23859800-23861000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:23859800-23862400	Enhancers	Pancreas	Pancrea
16	chr20:23860000-23860800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr20:23860000-23861200	Weak transcription	NHEK	skin
18	chr20:23860000-23861600	Enhancers	Rectal Smooth Muscle	rectum
19	chr20:23860000-23862200	Enhancers	HepG2	liver

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links