Variant report

Variant	rs3113880
Chromosome Location	chr4:48012042-48012043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10002498	0.87[ASN][1000 genomes]
rs10020447	0.87[ASN][1000 genomes]
rs1036681	0.87[ASN][1000 genomes]
rs10461075	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11732840	0.87[ASN][1000 genomes]
rs11946535	0.87[ASN][1000 genomes]
rs12506026	0.87[ASN][1000 genomes]
rs12647189	0.87[ASN][1000 genomes]
rs13143926	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440222	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1545200	0.87[ASN][1000 genomes]
rs1550444	0.87[ASN][1000 genomes]
rs1812964	0.87[ASN][1000 genomes]
rs188900	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1968542	0.87[ASN][1000 genomes]
rs1972883	0.87[ASN][1000 genomes]
rs1972884	0.87[ASN][1000 genomes]
rs2014934	0.87[ASN][1000 genomes]
rs2033895	0.87[ASN][1000 genomes]
rs2119204	0.87[ASN][1000 genomes]
rs2119207	0.87[ASN][1000 genomes]
rs2119208	0.87[ASN][1000 genomes]
rs224801	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352456	0.87[ASN][1000 genomes]
rs2352457	0.87[ASN][1000 genomes]
rs2352463	0.87[ASN][1000 genomes]
rs2352466	0.87[ASN][1000 genomes]
rs2581496	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28464733	0.87[ASN][1000 genomes]
rs2882950	0.87[ASN][1000 genomes]
rs3113877	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113879	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs321625	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs321639	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs321640	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs321641	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321647	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321649	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762858	0.87[ASN][1000 genomes]
rs3762859	0.87[ASN][1000 genomes]
rs3811761	0.87[ASN][1000 genomes]
rs3845160	0.87[ASN][1000 genomes]
rs4308343	0.87[ASN][1000 genomes]
rs4365692	0.87[ASN][1000 genomes]
rs4507330	0.87[ASN][1000 genomes]
rs4694868	0.87[ASN][1000 genomes]
rs4694871	0.87[ASN][1000 genomes]
rs4694878	0.87[ASN][1000 genomes]
rs4695287	0.87[ASN][1000 genomes]
rs4695302	0.87[ASN][1000 genomes]
rs4695309	0.87[ASN][1000 genomes]
rs4695312	0.87[ASN][1000 genomes]
rs6447596	0.87[ASN][1000 genomes]
rs6447599	0.87[ASN][1000 genomes]
rs6815975	0.87[ASN][1000 genomes]
rs6819506	0.87[ASN][1000 genomes]
rs6823572	0.87[ASN][1000 genomes]
rs6826190	0.87[ASN][1000 genomes]
rs6826909	0.87[ASN][1000 genomes]
rs6832334	0.87[ASN][1000 genomes]
rs6833320	0.87[ASN][1000 genomes]
rs6845451	0.87[ASN][1000 genomes]
rs707723	0.87[ASN][1000 genomes]
rs7668778	0.87[ASN][1000 genomes]
rs7670219	0.87[ASN][1000 genomes]
rs7672090	0.87[ASN][1000 genomes]
rs7690406	0.87[ASN][1000 genomes]
rs7690522	0.87[ASN][1000 genomes]
rs893861	0.87[ASN][1000 genomes]
rs893863	0.87[ASN][1000 genomes]
rs893864	0.87[ASN][1000 genomes]
rs920463	0.87[ASN][1000 genomes]
rs9291318	0.87[ASN][1000 genomes]
rs9291319	0.87[ASN][1000 genomes]
rs9995022	0.87[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
rs3113880	CNGA1	cis	Thyroid	GTEx
rs3113880	CNGA1	cis	Muscle Skeletal	GTEx
rs3113880	CNGA1	cis	Heart Left Ventricle	GTEx
rs3113880	CNGA1	cis	Esophagus Muscularis	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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