Variant report

Variant	rs1404289
Chromosome Location	chr3:134358109-134358110
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10804632	0.81[EUR][1000 genomes]
rs10935123	0.89[EUR][1000 genomes]
rs11915964	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11919458	0.80[EUR][1000 genomes]
rs11927539	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11927540	0.90[EUR][1000 genomes]
rs12637301	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13064209	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13071551	0.81[EUR][1000 genomes]
rs13075117	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13075253	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13076825	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13084192	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13088413	0.81[EUR][1000 genomes]
rs13089566	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13098546	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13322305	0.82[EUR][1000 genomes]
rs1357764	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1534025	0.81[EUR][1000 genomes]
rs1534029	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1534030	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1880374	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1880375	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1880378	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1880379	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1917130	0.81[EUR][1000 genomes]
rs2056603	0.82[EUR][1000 genomes]
rs2056604	0.82[EUR][1000 genomes]
rs2293293	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293294	0.90[EUR][1000 genomes]
rs2888670	0.91[EUR][1000 genomes]
rs4074521	0.90[EUR][1000 genomes]
rs4074522	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4074523	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4245903	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4245904	0.91[EUR][1000 genomes]
rs4245905	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4245907	0.89[EUR][1000 genomes]
rs4245908	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4306899	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4306900	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4318591	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4435681	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4435682	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4437193	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456908	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4519744	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4535271	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4543053	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605591	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4634170	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955468	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4955485	0.81[EUR][1000 genomes]
rs4955525	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955526	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955534	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4955542	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955544	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4955545	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955546	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4955547	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4955548	0.86[EUR][1000 genomes]
rs55835132	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58491661	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62269560	0.81[EUR][1000 genomes]
rs6763188	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764764	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6775611	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779294	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6779326	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6782563	0.81[EUR][1000 genomes]
rs6793487	0.81[EUR][1000 genomes]
rs6794258	0.89[EUR][1000 genomes]
rs6806810	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7430034	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7433991	0.82[EUR][1000 genomes]
rs7611611	0.82[EUR][1000 genomes]
rs7623567	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7626557	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7633868	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7641798	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642266	0.89[EUR][1000 genomes]
rs7648616	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7653807	0.88[EUR][1000 genomes]
rs7653880	0.89[EUR][1000 genomes]
rs9809344	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824185	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9836401	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9838119	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9838467	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9838621	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9838889	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9839705	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9841371	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846111	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9848254	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9851441	0.82[EUR][1000 genomes]
rs9857242	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9857995	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9864346	0.82[EUR][1000 genomes]
rs9871226	0.85[AMR][1000 genomes];0.97[EUR][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	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv877511	chr3:134174071-134358947	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv877512	chr3:134174071-134372486	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv877513	chr3:134174071-134379752	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv877514	chr3:134191938-134372486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv829730	chr3:134199097-134359544	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1404289	CEP63	cis	Esophagus Muscularis	GTEx
rs1404289	ANAPC13	cis	Artery Tibial	GTEx
rs1404289	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs1404289	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs1404289	ANAPC13	cis	Stomach	GTEx
rs1404289	ANAPC13	cis	Thyroid	GTEx
rs1404289	CEP63	cis	lung	GTEx
rs1404289	ANAPC13	cis	lung	GTEx
rs1404289	CEP63	cis	Artery Tibial	GTEx
rs1404289	ANAPC13	cis	multi-tissue	Pritchard
rs1404289	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs1404289	ANAPC13	cis	Nerve Tibial	GTEx
rs1404289	ANAPC13	cis	Muscle Skeletal	GTEx
rs1404289	ANAPC13	cis	Esophagus Muscularis	GTEx
rs1404289	CEP63	cis	Esophagus Mucosa	GTEx
rs1404289	ANAPC13	cis	Esophagus Mucosa	GTEx
rs1404289	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs1404289	ANAPC13	cis	Heart Left Ventricle	GTEx
rs1404289	ANAPC13	cis	Artery Aorta	GTEx
rs1404289	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134326000-134364800	Weak transcription	Osteobl	bone
2	chr3:134328200-134368200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:134330600-134360800	Weak transcription	Right Ventricle	heart
4	chr3:134335000-134358800	Weak transcription	Aorta	Aorta
5	chr3:134348000-134359800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:134348200-134363800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:134348400-134360800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:134354200-134361200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:134355600-134363200	Weak transcription	Psoas Muscle	Psoas
10	chr3:134356200-134361600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:134356800-134358600	Enhancers	Fetal Muscle Leg	muscle
12	chr3:134356800-134363400	Weak transcription	Fetal Intestine Small	intestine
13	chr3:134357400-134358400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:134357600-134359800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:134357800-134358200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:134357800-134359600	Weak transcription	Fetal Heart	heart
17	chr3:134358000-134358200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:134358000-134358200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:134358000-134358200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:134358000-134358400	Enhancers	Brain Anterior Caudate	brain
21	chr3:134358000-134358400	Enhancers	Brain Hippocampus Middle	brain
22	chr3:134358000-134358400	Enhancers	HSMMtube	muscle
23	chr3:134358000-134358600	Enhancers	HepG2	liver

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