Variant report

Variant	rs11147404
Chromosome Location	chr13:30539456-30539457
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041577	0.82[TSI][hapmap]
rs11841228	0.93[ASN][1000 genomes]
rs12429187	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12429599	0.98[ASN][1000 genomes]
rs12430579	0.98[ASN][1000 genomes]
rs12584184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584938	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17074118	0.82[MEX][hapmap];0.88[TSI][hapmap]
rs2039952	0.98[ASN][1000 genomes]
rs4769789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs481209	1.00[ASN][1000 genomes]
rs501259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502203	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502944	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512583	0.80[CHB][hapmap]
rs533219	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553661	1.00[ASN][1000 genomes]
rs564388	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566495	0.80[CHB][hapmap]
rs576712	0.93[ASN][1000 genomes]
rs641826	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643508	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644413	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6490436	0.89[ASN][1000 genomes]
rs6490437	0.90[ASN][1000 genomes]
rs649164	0.86[ASN][1000 genomes]
rs655338	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66986978	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73159331	0.94[ASN][1000 genomes]
rs73159342	0.98[ASN][1000 genomes]
rs7327777	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332851	0.90[ASN][1000 genomes]
rs7333780	0.96[ASN][1000 genomes]
rs7334559	0.93[ASN][1000 genomes]
rs7334714	0.93[ASN][1000 genomes]
rs7358905	0.97[ASN][1000 genomes]
rs7982470	0.98[ASN][1000 genomes]
rs7982637	0.97[ASN][1000 genomes]
rs7983558	0.98[ASN][1000 genomes]
rs7990062	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9314992	0.92[ASN][1000 genomes]
rs9551791	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11147404	SNORA27	cis	cerebellum	SCAN
rs11147404	UBL3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30537800-30539600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr13:30538600-30539800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:30539000-30539800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr13:30539200-30539600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:30539200-30539600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr13:30539200-30539800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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