Variant report

Variant	rs321644
Chromosome Location	chr4:48008308-48008309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002500	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10461076	0.85[ASN][1000 genomes]
rs10517200	1.00[CEU][hapmap]
rs10517204	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs10805163	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs11733288	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12504018	0.91[YRI][hapmap]
rs12645164	1.00[CEU][hapmap]
rs12645245	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs12651301	0.91[YRI][hapmap]
rs1371729	0.95[YRI][hapmap]
rs1371732	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1396051	0.87[JPT][hapmap];0.86[YRI][hapmap]
rs1440228	0.91[YRI][hapmap]
rs1507913	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507914	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178650	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1837518	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866688	1.00[CEU][hapmap]
rs1866689	0.91[YRI][hapmap]
rs188901	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352470	0.95[YRI][hapmap]
rs2581493	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2661513	0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28642966	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs28699496	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3113881	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113882	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321621	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321623	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs321633	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs321642	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950558	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4694880	0.87[JPT][hapmap];0.83[YRI][hapmap]
rs4695326	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6447603	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6823184	0.91[YRI][hapmap]
rs6823698	0.91[YRI][hapmap]
rs6850603	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6858440	0.91[YRI][hapmap]
rs978094	0.91[YRI][hapmap]
rs9995122	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS 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	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs321644	CNGA1	cis	Muscle Skeletal	GTEx
rs321644	NFXL1	cis	Whole Blood	GTEx
rs321644	CORIN	cis	Whole Blood	GTEx
rs321644	CNGA1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48005200-48011200	Weak transcription	Liver	Liver
2	chr4:48005400-48017400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:48006400-48013000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr4:48007400-48013200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr4:48007600-48013000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
6	chr4:48008000-48017600	Weak transcription	Psoas Muscle	Psoas

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