Variant report

Variant	rs12115487
Chromosome Location	chr9:14723828-14723829
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10961658	1.00[YRI][hapmap]
rs10961679	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11793334	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11794846	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12115314	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16932231	1.00[ASN][1000 genomes]
rs17289263	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17290109	1.00[YRI][hapmap]
rs2131882	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2131883	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2182855	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv933345	chr9:14695436-14750474	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv892614	chr9:14712257-14756969	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12115487	CER1	cis	Nerve Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14717800-14746200	Weak transcription	Pancreas	Pancrea
2	chr9:14722400-14724000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:14722600-14726400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:14723000-14724200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr9:14723200-14724000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr9:14723200-14724200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
7	chr9:14723400-14724000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:14723400-14724000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:14723600-14724000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr9:14723600-14724200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr9:14723600-14730800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:14723800-14724200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:14723800-14724800	Enhancers	H1 BMP4 Derived Mesendoderm 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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