Variant report

Variant	rs1968542
Chromosome Location	chr4:47956139-47956140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10002498	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020447	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036681	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.88[EUR][1000 genomes]
rs10938508	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11732840	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1371728	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1440222	1.00[ASN][1000 genomes]
rs1545200	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550444	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808853	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1812964	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.90[EUR][1000 genomes]
rs2033895	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119204	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.84[EUR][1000 genomes]
rs2119207	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2352456	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs321640	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs321641	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3762858	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762859	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694868	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694875	0.89[EUR][1000 genomes]
rs4694878	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.85[EUR][1000 genomes]
rs4695296	0.90[EUR][1000 genomes]
rs4695302	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695309	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.97[EUR][1000 genomes]
rs6447596	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6815975	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819506	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826909	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832334	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833320	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845451	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707723	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672090	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893861	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291318	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv967291	chr4:47954000-47981934	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1968542	CNGA1	cis	Esophagus Muscularis	GTEx
rs1968542	CNGA1	cis	Heart Left Ventricle	GTEx
rs1968542	CNGA1	cis	Muscle Skeletal	GTEx
rs1968542	CNGA1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47954600-47959200	Weak transcription	Right Atrium	heart
2	chr4:47956000-47956600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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