Variant report

Variant	rs12420703
Chromosome Location	chr11:45690568-45690569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1026078	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769158	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10769159	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838504	0.90[AFR][1000 genomes]
rs11603055	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012019	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148894	0.97[AFR][1000 genomes]
rs4148895	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148899	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4148901	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs737244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs895733	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895734	1.00[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897311	chr11:45663568-45691118	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv897312	chr11:45663568-45699134	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv897313	chr11:45670395-45699134	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv467870	chr11:45684557-45757401	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv554199	chr11:45684557-45757401	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12420703	OR4C45	cis	cerebellum	SCAN
rs12420703	CHST1	cis	parietal	SCAN
rs12420703	F2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45687200-45699000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45687600-45692000	Weak transcription	Pancreas	Pancrea
3	chr11:45687800-45692400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:45688000-45700600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:45688800-45692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:45688800-45692800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:45688800-45692800	Weak transcription	Brain Anterior Caudate	brain
8	chr11:45688800-45692800	Weak transcription	Brain Substantia Nigra	brain
9	chr11:45688800-45693200	Weak transcription	Brain Angular Gyrus	brain
10	chr11:45688800-45693200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:45689000-45690600	Enhancers	Fetal Muscle Leg	muscle
12	chr11:45689000-45692200	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:45689000-45693200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:45690000-45690600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr11:45690400-45690800	Enhancers	HUVEC	blood vessel

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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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