Variant report

Variant	rs7419516
Chromosome Location	chr2:56403345-56403346
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11674133	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13034898	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1814276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1861773	0.93[ASN][1000 genomes]
rs2216328	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4671275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672096	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs6735241	0.89[ASN][1000 genomes]
rs7576331	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs960489	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs960490	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[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	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7419516	DCLK3	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56398800-56406000	Weak transcription	Adipose Nuclei	Adipose
2	chr2:56398800-56409200	Weak transcription	Placenta	Placenta
3	chr2:56399600-56404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:56400400-56410200	Weak transcription	HUVEC	blood vessel
5	chr2:56401000-56410600	Weak transcription	Left Ventricle	heart
6	chr2:56402400-56403400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:56403000-56403400	Enhancers	H9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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