Variant report

Variant	rs416842
Chromosome Location	chr20:15639525-15639526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1420433	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2023386	0.83[CEU][hapmap]
rs417099	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs455709	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs456022	0.83[EUR][1000 genomes]
rs456544	0.89[CEU][hapmap]
rs460411	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460818	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs465374	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs465416	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs465525	0.85[CEU][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs465981	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6034249	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs6034250	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6043422	0.85[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]

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	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2751909	chr20:15489871-15656007	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv833928	chr20:15619962-15780758	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15634000-15641200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:15637200-15640800	Weak transcription	NHDF-Ad	bronchial
3	chr20:15638800-15639600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:15638800-15640200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr20:15638800-15640600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:15639000-15639600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr20:15639000-15639600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:15639000-15639600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr20:15639000-15639600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr20:15639000-15639600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:15639000-15640200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:15639200-15639600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr20:15639200-15639600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr20:15639200-15639600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr20:15639400-15639600	Enhancers	Brain Anterior Caudate	brain
16	chr20:15639400-15639600	Enhancers	Brain Cingulate Gyrus	brain
17	chr20:15639400-15639600	Enhancers	Brain Hippocampus Middle	brain
18	chr20:15639400-15639800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:15639400-15640000	Enhancers	Brain Substantia Nigra	brain

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