Variant report

Variant	rs10877220
Chromosome Location	chr12:59562598-59562599
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10747833	0.88[EUR][1000 genomes]
rs10783945	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10877217	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10877218	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10877219	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10877221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10877229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10877230	0.96[EUR][1000 genomes]
rs10877232	0.95[EUR][1000 genomes]
rs10877237	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10877244	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10877245	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10877249	0.90[EUR][1000 genomes]
rs10877261	0.88[EUR][1000 genomes]
rs11172923	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11172925	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11172948	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172949	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172950	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172969	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172970	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11172974	0.93[EUR][1000 genomes]
rs11614578	0.87[EUR][1000 genomes]
rs12322225	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12371751	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12371777	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12372677	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2036303	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2063846	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66833395	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1050375	chr12:59550900-59655366	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv832430	chr12:59552811-59658333	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1039996	chr12:59556074-59645306	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10877220	OR6C2	cis	parietal	SCAN
rs10877220	AVIL	cis	cerebellum	SCAN
rs10877220	MESP2	trans	cerebellum	SCAN
rs10877220	STAT6	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59559600-59562800	Enhancers	Fetal Intestine Large	intestine
2	chr12:59560400-59563200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:59561800-59562800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:59561800-59562800	Enhancers	Fetal Brain Female	brain
5	chr12:59562200-59562800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:59562200-59563000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:59562400-59562800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:59562400-59562800	Enhancers	Brain Germinal Matrix	brain

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