Variant report

Variant	rs188901
Chromosome Location	chr4:48011812-48011813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10461076	0.83[ASN][1000 genomes]
rs11733288	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12645245	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1507913	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1507914	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178650	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1837518	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899060	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs224800	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581493	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2661513	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28699496	0.88[ASN][1000 genomes]
rs3113881	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113882	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs321621	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs321623	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs321633	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs321642	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321644	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321646	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3950558	0.88[ASN][1000 genomes]
rs4695326	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6850603	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]

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
rs188901	CNGA1	cis	Muscle Skeletal	GTEx
rs188901	NFXL1	cis	Whole Blood	GTEx
rs188901	CNGA1	cis	Nerve Tibial	GTEx
rs188901	CORIN	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48005400-48017400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:48006400-48013000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr4:48007400-48013200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr4:48007600-48013000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
5	chr4:48008000-48017600	Weak transcription	Psoas Muscle	Psoas
6	chr4:48008600-48013800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
7	chr4:48009200-48012800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
8	chr4:48010200-48017200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:48010200-48017600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:48010600-48012600	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr4:48010600-48014400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:48011000-48017400	Weak transcription	Colonic Mucosa	Colon
13	chr4:48011000-48017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:48011000-48017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:48011200-48013000	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr4:48011200-48013200	Strong transcription	Liver	Liver
17	chr4:48011200-48017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:48011400-48017600	Weak transcription	Esophagus	oesophagus
19	chr4:48011600-48013000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr4:48011800-48017800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:48011800-48018200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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