Variant report

Variant	rs2408694
Chromosome Location	chr13:53538323-53538324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11617841	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs1407751	0.81[ASN][1000 genomes]
rs1407752	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1407753	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1885849	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2181473	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4301922	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4301923	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4301924	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4562966	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4562967	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5026013	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58811753	0.81[ASN][1000 genomes]
rs59849453	0.81[ASN][1000 genomes]
rs67378042	0.81[ASN][1000 genomes]
rs68176651	0.81[ASN][1000 genomes]
rs7140120	0.80[EUR][1000 genomes]
rs7320217	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7323033	0.87[EUR][1000 genomes];0.83[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	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2408694	ITM2B	cis	cerebellum	SCAN
rs2408694	CCDC70	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53532800-53541000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:53533800-53540800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:53534800-53539000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr13:53535000-53538600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr13:53536800-53538800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:53537600-53538400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr13:53537600-53538600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:53537600-53539200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:53537800-53538600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr13:53537800-53538600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:53537800-53538600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr13:53537800-53538600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:53538000-53538600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr13:53538200-53538400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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