Variant report

Variant	rs6561690
Chromosome Location	chr13:53467535-53467536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1980691	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6561690	OLFM4	cis	cerebellum	SCAN
rs6561690	DLEU1	cis	cerebellum	SCAN
rs6561690	DLEU7	cis	parietal	SCAN
rs6561690	CAB39L	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53461600-53471200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:53463000-53471200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:53466000-53468400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:53466400-53471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:53466800-53471000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:53466800-53471200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:53466800-53472400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:53467000-53469600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53467000-53471000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr13:53467200-53467600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:53467200-53468000	Weak transcription	Fetal Brain Male	brain
12	chr13:53467200-53471000	Weak transcription	Fetal Brain Female	brain
13	chr13:53467400-53469800	Weak transcription	Fetal Stomach	stomach
14	chr13:53467400-53471000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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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

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