Variant report

Variant	rs12788284
Chromosome Location	chr11:49238090-49238091
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1164657	0.80[ASN][1000 genomes]
rs12099184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573896	0.87[ASN][1000 genomes]
rs12574928	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12577182	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12790852	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12797369	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12801054	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12806285	0.80[ASN][1000 genomes]
rs12806991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906205	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17743650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202694	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs202706	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202715	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202718	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202721	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2299649	0.87[ASN][1000 genomes]
rs2903311	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34279527	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34397699	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34460216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34534443	0.80[ASN][1000 genomes]
rs34913116	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34966829	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35416991	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35777887	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35839246	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs36067143	0.89[ASN][1000 genomes]
rs383028	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3862341	0.80[ASN][1000 genomes]
rs3903422	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57165791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583850	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617528	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs646131	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67736905	0.83[ASN][1000 genomes]
rs71477493	0.83[ASN][1000 genomes]
rs71477497	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71477498	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71479304	0.80[ASN][1000 genomes]
rs71479305	0.80[ASN][1000 genomes]
rs72908309	0.84[AMR][1000 genomes];0.91[ASN][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	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	nsv972015	chr11:49187522-49240719	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv1834726	chr11:49215288-49242990	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12788284	NR1H3	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:49235200-49238400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:49236400-49242400	Weak transcription	Brain Substantia Nigra	brain

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