Variant report

Variant	rs10747833
Chromosome Location	chr12:59707258-59707259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10783945	0.93[EUR][1000 genomes]
rs10877217	0.86[EUR][1000 genomes]
rs10877218	0.88[EUR][1000 genomes]
rs10877219	0.88[EUR][1000 genomes]
rs10877220	0.88[EUR][1000 genomes]
rs10877221	0.88[EUR][1000 genomes]
rs10877229	0.91[EUR][1000 genomes]
rs10877230	0.90[EUR][1000 genomes]
rs10877232	0.89[EUR][1000 genomes]
rs10877237	0.93[EUR][1000 genomes]
rs10877244	0.93[EUR][1000 genomes]
rs10877245	0.90[EUR][1000 genomes]
rs10877249	0.92[EUR][1000 genomes]
rs10877261	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172923	0.84[EUR][1000 genomes]
rs11172925	0.87[EUR][1000 genomes]
rs11172948	0.93[EUR][1000 genomes]
rs11172949	0.93[EUR][1000 genomes]
rs11172950	0.93[EUR][1000 genomes]
rs11172969	0.95[EUR][1000 genomes]
rs11172970	0.95[EUR][1000 genomes]
rs11172974	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11172999	0.84[EUR][1000 genomes]
rs11173007	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11173010	0.82[EUR][1000 genomes]
rs11614578	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12322225	0.88[EUR][1000 genomes]
rs12371751	0.81[EUR][1000 genomes]
rs12371777	0.81[EUR][1000 genomes]
rs12372677	0.90[EUR][1000 genomes]
rs2036303	0.93[EUR][1000 genomes]
rs2063846	0.88[EUR][1000 genomes]
rs2175949	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2221986	0.82[EUR][1000 genomes]
rs28873799	0.80[AMR][1000 genomes]
rs58032918	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66833395	0.93[EUR][1000 genomes]
rs73121904	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1054961	chr12:59516659-59764209	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv541506	chr12:59516659-59764209	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv559052	chr12:59532203-59809256	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1051696	chr12:59622403-59741106	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv899128	chr12:59636969-59766169	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv559054	chr12:59671388-59735221	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv520767	chr12:59671388-59782228	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10747833	MESP2	trans	cerebellum	SCAN
rs10747833	OR6C2	cis	parietal	SCAN
rs10747833	HOXC6	cis	parietal	SCAN
rs10747833	AVIL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59704600-59707400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59705400-59707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:59707200-59709000	Enhancers	Brain Germinal Matrix	brain

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