Variant report

Variant	rs4955544
Chromosome Location	chr3:134332776-134332777
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10804632	0.82[EUR][1000 genomes]
rs10935123	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11915964	0.87[EUR][1000 genomes]
rs11919458	0.81[EUR][1000 genomes]
rs11927539	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11927540	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637301	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13064209	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13071551	0.82[EUR][1000 genomes]
rs13075117	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075253	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13076825	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13084192	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13088413	0.82[EUR][1000 genomes]
rs13089566	0.87[EUR][1000 genomes]
rs13098546	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13322305	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1357764	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1404289	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1534025	0.82[EUR][1000 genomes]
rs1534029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534030	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880374	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880375	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880378	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1917130	0.82[EUR][1000 genomes]
rs2056603	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2056604	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2293293	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293294	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2888670	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074521	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074522	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074523	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245903	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245904	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245907	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4245908	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4306899	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4306900	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4318591	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435681	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4435682	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4437193	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4456908	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4519744	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4535271	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4543053	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4605591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634170	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4955468	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955485	0.82[EUR][1000 genomes]
rs4955525	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955526	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955534	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955542	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955545	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955546	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955547	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4955548	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55835132	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58491661	0.87[EUR][1000 genomes]
rs62269560	0.82[EUR][1000 genomes]
rs6763188	0.87[EUR][1000 genomes]
rs6764764	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775611	0.87[EUR][1000 genomes]
rs6779294	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779326	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782563	0.82[EUR][1000 genomes]
rs6793487	0.82[EUR][1000 genomes]
rs6794258	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6806810	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430034	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7433991	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7611611	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7623567	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626557	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633868	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641798	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7642266	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7648616	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653807	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7653880	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9809344	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824185	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836401	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9838119	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838467	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838621	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839705	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841371	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9846111	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851441	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9857242	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9857995	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9864346	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9871226	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
7	nsv1002382	chr3:134239191-134358001	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4955544	ANAPC13	cis	Nerve Tibial	GTEx
rs4955544	ANAPC13	cis	Esophagus Mucosa	GTEx
rs4955544	ANAPC13	cis	Muscle Skeletal	GTEx
rs4955544	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs4955544	CEP63	cis	Artery Tibial	GTEx
rs4955544	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs4955544	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs4955544	CEP63	cis	Esophagus Muscularis	GTEx
rs4955544	CEP63	cis	Esophagus Mucosa	GTEx
rs4955544	ANAPC13	cis	lung	GTEx
rs4955544	ANAPC13	cis	multi-tissue	Pritchard
rs4955544	ANAPC13	cis	Artery Tibial	GTEx
rs4955544	ANAPC13	cis	Heart Left Ventricle	GTEx
rs4955544	ANAPC13	cis	Stomach	GTEx
rs4955544	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs4955544	ANAPC13	cis	Esophagus Muscularis	GTEx
rs4955544	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs4955544	ANAPC13	cis	Thyroid	GTEx
rs4955544	CEP63	cis	lung	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134319600-134334600	Weak transcription	Aorta	Aorta
2	chr3:134319800-134353800	Weak transcription	Left Ventricle	heart
3	chr3:134320400-134338000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:134321200-134335200	Weak transcription	Ovary	ovary
5	chr3:134321600-134336800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:134321600-134349200	Weak transcription	Brain Substantia Nigra	brain
7	chr3:134321800-134337400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:134321800-134337800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:134324800-134333200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:134326000-134364800	Weak transcription	Osteobl	bone
11	chr3:134326200-134340200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:134327200-134339000	Weak transcription	Spleen	Spleen
13	chr3:134327200-134340000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:134327400-134338400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:134328200-134368200	Weak transcription	Brain Angular Gyrus	brain
16	chr3:134328600-134333400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:134329400-134336800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:134329400-134349000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:134329600-134340000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:134330200-134356800	Weak transcription	Fetal Heart	heart
21	chr3:134330400-134339800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:134330600-134360800	Weak transcription	Right Ventricle	heart
23	chr3:134331000-134334000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:134331400-134333600	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:134331400-134349000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:134331600-134336600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:134332000-134336400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:134332000-134336600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:134332000-134336600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:134332200-134336600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:134332400-134336400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:134332400-134340600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:134332400-134342000	Weak transcription	Psoas Muscle	Psoas
34	chr3:134332400-134347800	Weak transcription	Colon Smooth Muscle	Colon

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