Variant report

Variant	rs1412133
Chromosome Location	chr1:79796966-79796967
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10732727	0.90[AMR][1000 genomes]
rs10735756	0.84[AMR][1000 genomes]
rs10735757	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747361	0.81[AMR][1000 genomes]
rs10874032	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11162678	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162684	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11162685	0.88[AMR][1000 genomes]
rs11162686	0.96[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs12127263	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143992	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331707	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1331709	0.89[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1331713	0.81[AMR][1000 genomes]
rs1331718	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1412129	0.90[AMR][1000 genomes]
rs1412130	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1412131	0.90[AMR][1000 genomes]
rs1412132	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412134	0.90[AMR][1000 genomes]
rs1412135	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1412137	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1412139	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1888766	0.90[AMR][1000 genomes]
rs1929622	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2039339	0.84[AMR][1000 genomes]
rs2882993	0.90[AMR][1000 genomes]
rs2989850	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015124	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3015126	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3915745	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5012068	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6424649	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515632	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7528017	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7542083	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7546200	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7553187	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[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	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv871182	chr1:79614989-79822735	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870962	chr1:79755185-79835066	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3364783	chr1:79786074-79815088	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	esv3384616	chr1:79788134-79814492	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	nsv830337	chr1:79791879-79913241	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv546633	chr1:79794719-79877035	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1412133	SNORD45C	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79794000-79798400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:79795600-79797400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:79795600-79797600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:79795800-79798400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:79796600-79801400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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