Variant report

Variant	rs12699012
Chromosome Location	chr7:70782376-70782377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10224696	0.89[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10240080	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10252095	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10263419	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10281560	0.86[EUR][1000 genomes]
rs12532253	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12532676	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12540683	0.89[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12699007	0.89[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12699008	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12699009	0.89[CEU][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12699010	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12699011	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12699013	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12699032	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1558002	0.81[CEU][hapmap]
rs17143419	0.88[CEU][hapmap]
rs1882573	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2707422	0.82[EUR][1000 genomes]
rs34702051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35182494	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4305790	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4323379	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56340632	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62462185	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62462209	0.81[EUR][1000 genomes]
rs6949288	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71549400	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7799967	0.92[TSI][hapmap]
rs7803373	0.89[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12699012	CCDC18	trans	cerebellum	SCAN
rs12699012	FZD9	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70765800-70790000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:70773400-70789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:70777000-70788800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:70778800-70784400	Weak transcription	Brain Anterior Caudate	brain
5	chr7:70780800-70789200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:70781200-70782600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:70782000-70782400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:70782000-70782600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:70782200-70782400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr7:70782200-70782600	Enhancers	Pancreas	Pancrea

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