Variant report

Variant	rs598101
Chromosome Location	chr11:49246979-49246980
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10839239	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs175849	0.83[EUR][1000 genomes]
rs182168	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs202669	0.81[EUR][1000 genomes]
rs202671	0.81[EUR][1000 genomes]
rs202674	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs202675	0.84[ASN][1000 genomes]
rs202676	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs202677	0.87[ASN][1000 genomes]
rs202678	0.84[ASN][1000 genomes]
rs202682	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs202683	0.82[ASN][1000 genomes]
rs202684	0.82[ASN][1000 genomes]
rs202685	0.82[ASN][1000 genomes]
rs202690	0.82[EUR][1000 genomes]
rs202692	0.84[EUR][1000 genomes]
rs202702	0.82[EUR][1000 genomes]
rs202703	0.84[EUR][1000 genomes]
rs202707	0.81[EUR][1000 genomes]
rs2866098	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35580985	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35746327	0.84[ASN][1000 genomes]
rs607065	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs608314	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611414	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs611816	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs635976	0.89[ASN][1000 genomes]
rs644754	0.81[EUR][1000 genomes]
rs647370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs648372	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs660439	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs660476	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs664584	0.81[EUR][1000 genomes]
rs667827	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs670039	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs670776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][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	nsv469956	chr11:48922645-49862647	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv554347	chr11:49111467-49862647	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1044070	chr11:49147743-49448774	Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv525454	chr11:49156039-49570587	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv518571	chr11:49162948-49627833	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758269	chr11:49212237-49468966	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2759825	chr11:49212237-49468966	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv972016	chr11:49246163-49330536	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs598101	OR4C3	cis	parietal	SCAN
rs598101	LOC441601	cis	cerebellum	SCAN
rs598101	MTCH2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:49245200-49254600	Weak transcription	Fetal Intestine Small	intestine
2	chr11:49245400-49251000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:49245600-49247600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr11:49246400-49247400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:49246600-49247200	Enhancers	Brain Hippocampus Middle	brain
6	chr11:49246800-49247000	Enhancers	Brain Inferior Temporal Lobe	brain

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