Variant report

Variant	rs2762924
Chromosome Location	chr20:52756548-52756549
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2585413	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2616276	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2762923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2762924	CYP24A1	cis	parietal	SCAN
rs2762924	KCNG1	cis	cerebellum	SCAN
rs2762924	TFAP2C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52750200-52756600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:52751000-52756600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr20:52751200-52758000	Weak transcription	Placenta	Placenta
4	chr20:52751400-52757000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:52751400-52757200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr20:52751400-52758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:52754000-52758400	Enhancers	HepG2	liver
8	chr20:52755600-52757000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:52755600-52758400	Enhancers	NHEK	skin
10	chr20:52755600-52758600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:52755600-52758600	Enhancers	NH-A	brain
12	chr20:52755600-52758800	Enhancers	HMEC	breast
13	chr20:52755600-52759000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:52755800-52758200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr20:52756000-52757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:52756000-52758600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:52756200-52757400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:52756200-52758000	Enhancers	A549	lung
19	chr20:52756200-52758200	Enhancers	HSMM	muscle

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