Variant report

Variant	rs4886021
Chromosome Location	chr13:53466127-53466128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11617253	0.99[ASN][1000 genomes]
rs12100317	0.95[ASN][1000 genomes]
rs2236363	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs3742300	0.90[ASN][1000 genomes]
rs3742301	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4143183	0.95[ASN][1000 genomes]
rs582583	0.80[ASN][1000 genomes]
rs61950421	0.99[ASN][1000 genomes]
rs67683610	0.99[ASN][1000 genomes]
rs9788389	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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv900090	chr13:53429453-53495715	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886021	RB1	cis	parietal	SCAN
rs4886021	DLEU1	cis	cerebellum	SCAN
rs4886021	MLNR	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53453200-53466600	Weak transcription	Fetal Brain Female	brain
2	chr13:53461600-53471200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:53462000-53467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53463000-53471200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:53465400-53466400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr13:53465400-53466600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:53465400-53467400	Enhancers	Stomach Mucosa	stomach
8	chr13:53465600-53466800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr13:53465600-53466800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr13:53465600-53467000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:53465600-53467000	Weak transcription	Gastric	stomach
12	chr13:53465600-53467200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr13:53465800-53466200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr13:53465800-53466400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr13:53465800-53467000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr13:53466000-53468400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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

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