Variant report

Variant	rs17836240
Chromosome Location	chr14:69953961-69953962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10131446	0.89[AMR][1000 genomes]
rs10132626	0.85[ASW][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10137655	1.00[CHD][hapmap];0.90[LWK][hapmap]
rs10137668	1.00[CHD][hapmap];0.92[LWK][hapmap]
rs11158808	1.00[CHD][hapmap]
rs11847666	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17764155	0.85[ASW][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2015547	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28531897	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6573886	0.88[AMR][1000 genomes]
rs7161463	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8016334	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	esv3396933	chr14:69906914-70001258	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1048882	chr14:69920881-69976694	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052107	chr14:69922552-69969297	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1039230	chr14:69922552-69972002	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1039192	chr14:69922552-69976694	Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv456335	chr14:69928307-69971598	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv564967	chr14:69928307-69971598	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1050258	chr14:69942127-69976694	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17836240	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL
rs17836240	C14orf181	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69953400-69954200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:69953600-69955000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:69953800-69955200	Enhancers	H9 Derived Neuron 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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