Variant report

Variant	rs2071445
Chromosome Location	chr20:23857982-23857983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1799841	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2071443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285059	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6076157	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[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	esv3411629	chr20:23855752-23860150	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071445	PLK1S1	cis	parietal	SCAN
rs2071445	CST5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23848800-23860400	Enhancers	Fetal Thymus	thymus
2	chr20:23851400-23859400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23852400-23864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:23852800-23858200	Enhancers	Dnd41	blood
5	chr20:23854600-23858200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:23854800-23860600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr20:23855400-23858000	Weak transcription	Spleen	Spleen
8	chr20:23855400-23858200	Enhancers	Fetal Stomach	stomach
9	chr20:23857400-23860600	Weak transcription	Colon Smooth Muscle	Colon
10	chr20:23857600-23858000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr20:23857600-23858200	Weak transcription	Fetal Intestine Large	intestine
12	chr20:23857800-23858000	Enhancers	Rectal Smooth Muscle	rectum

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