Variant report

Variant	rs11723646
Chromosome Location	chr4:47706607-47706608
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13122612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148518	0.92[ASN][1000 genomes]
rs16860610	1.00[YRI][hapmap]
rs16860620	1.00[YRI][hapmap]
rs17572939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36050129	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4473628	0.83[GIH][hapmap]
rs61762931	0.92[ASN][1000 genomes]
rs6813519	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825078	0.91[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs6849926	0.86[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs71614008	0.92[ASN][1000 genomes]
rs73238629	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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 miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	nsv829924	chr4:47670905-47866665	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv879007	chr4:47688064-47752554	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11723646	CNGA1	cis	Muscle Skeletal	GTEx
rs11723646	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47646400-47707400	Weak transcription	Right Ventricle	heart
2	chr4:47703000-47706800	Weak transcription	Left Ventricle	heart
3	chr4:47704400-47709600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:47705200-47707800	Enhancers	Fetal Lung	lung
5	chr4:47705400-47707000	Enhancers	Fetal Heart	heart
6	chr4:47706000-47706800	Enhancers	Fetal Kidney	kidney
7	chr4:47706000-47706800	Bivalent Enhancer	HepG2	liver
8	chr4:47706200-47707200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:47706200-47707600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:47706200-47707600	Flanking Active TSS	Liver	Liver
11	chr4:47706600-47707200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:47706600-47707200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:47706600-47707200	Enhancers	Psoas Muscle	Psoas
14	chr4:47706600-47707400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:47706600-47708200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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