Variant report

Variant	rs4471413
Chromosome Location	chr11:4731583-4731584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1032446	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1032448	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10500613	0.87[CHB][hapmap]
rs10500615	0.93[CEU][hapmap];0.84[CHD][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10734440	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs10768185	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10836495	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs10836500	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836503	0.91[EUR][1000 genomes]
rs10836521	0.92[EUR][1000 genomes]
rs11033409	0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11033428	0.91[EUR][1000 genomes]
rs11033454	0.86[ASN][1000 genomes]
rs11033474	0.89[EUR][1000 genomes]
rs11033480	0.91[EUR][1000 genomes]
rs11033491	0.92[EUR][1000 genomes]
rs11033495	0.92[EUR][1000 genomes]
rs11033496	0.92[EUR][1000 genomes]
rs11033517	0.88[EUR][1000 genomes]
rs11033521	0.88[EUR][1000 genomes]
rs11600164	0.90[EUR][1000 genomes]
rs12222503	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12271916	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12277885	0.91[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs12577711	0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs1389462	0.89[EUR][1000 genomes]
rs1493743	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1493745	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs1565762	0.84[ASN][1000 genomes]
rs16932124	0.93[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs16932578	0.93[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs16933260	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs16933304	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs16933308	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs16933600	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1845362	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs4255531	0.94[ASN][1000 genomes]
rs4284391	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4331086	0.92[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382899	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4432013	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4436535	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4463838	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4465362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4562822	0.88[EUR][1000 genomes]
rs4619142	1.00[ASN][1000 genomes]
rs57437632	0.99[ASN][1000 genomes]
rs61681282	0.99[ASN][1000 genomes]
rs7108910	0.86[ASN][1000 genomes]
rs7112068	0.84[ASN][1000 genomes]
rs7112203	0.84[ASN][1000 genomes]
rs7123544	0.84[ASN][1000 genomes]
rs7124586	0.92[EUR][1000 genomes]
rs7478759	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043803	chr11:4388448-4837042	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv540916	chr11:4388448-4837042	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1048224	chr11:4390227-4920324	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv540917	chr11:4390227-4920324	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv896911	chr11:4400801-4806872	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv832055	chr11:4550894-4736340	Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv3424302	chr11:4585155-4880050	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
9	nsv896915	chr11:4659419-4844393	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv832056	chr11:4673001-4824890	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1046486	chr11:4697151-4741730	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
12	nsv896916	chr11:4712353-4806872	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv437699	chr11:4721204-4741954	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4471413	SNORA52	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4726200-4734200	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:4726800-4734200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:4727000-4734200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:4731200-4731600	ZNF genes & repeats	Aorta	Aorta

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