Variant report

Variant	rs4519744
Chromosome Location	chr3:134321523-134321524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134314944..134317745-chr3:134318153..134321546,4	K562	blood:

Variant related genes	Relation type
ENSG00000154928	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10804632	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935123	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11915964	0.81[EUR][1000 genomes]
rs11919458	0.87[EUR][1000 genomes]
rs11927539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927540	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064209	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13071551	0.88[EUR][1000 genomes]
rs13075117	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075253	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13076825	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13084192	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13088413	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13089566	0.81[EUR][1000 genomes]
rs13098546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13322305	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1357764	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1404289	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1534025	0.88[EUR][1000 genomes]
rs1534029	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534030	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880375	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880378	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880379	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1917130	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2056603	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2056604	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2293293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293294	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888670	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4074521	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4074522	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4074523	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245905	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245907	0.81[EUR][1000 genomes]
rs4245908	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4306899	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4306900	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4318591	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4435681	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4435682	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4437193	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4456908	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535271	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543053	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4605591	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4634170	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4955468	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955485	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4955525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955542	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955544	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955545	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4955546	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955547	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4955548	0.82[ASN][1000 genomes]
rs55835132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56899746	0.86[EUR][1000 genomes]
rs58491661	0.81[EUR][1000 genomes]
rs58808286	0.84[EUR][1000 genomes]
rs62269560	0.88[EUR][1000 genomes]
rs6763188	0.81[EUR][1000 genomes]
rs6764764	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6775611	0.81[EUR][1000 genomes]
rs6779294	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782563	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793487	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6794258	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806810	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7430034	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7433991	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7611611	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623567	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633868	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641798	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642266	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7648616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653807	0.82[ASN][1000 genomes]
rs7653880	0.81[EUR][1000 genomes]
rs9756173	0.83[EUR][1000 genomes]
rs9809344	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836401	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9838119	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838467	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838621	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838889	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9841371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9846111	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848254	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851441	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9857242	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864346	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9871226	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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
rs4519744	ANAPC13	cis	Muscle Skeletal	GTEx
rs4519744	ANAPC13	cis	Esophagus Mucosa	GTEx
rs4519744	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs4519744	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs4519744	CEP63	cis	lung	GTEx
rs4519744	ANAPC13	cis	multi-tissue	Pritchard
rs4519744	CEP63	cis	Esophagus Mucosa	GTEx
rs4519744	ANAPC13	cis	Artery Aorta	GTEx
rs4519744	ANAPC13	cis	Artery Tibial	GTEx
rs4519744	ANAPC13	cis	Esophagus Muscularis	GTEx
rs4519744	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs4519744	CEP63	cis	Artery Tibial	GTEx
rs4519744	ANAPC13	cis	lung	GTEx
rs4519744	ANAPC13	cis	Nerve Tibial	GTEx
rs4519744	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs4519744	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs4519744	CEP63	cis	Esophagus Muscularis	GTEx
rs4519744	ANAPC13	cis	Stomach	GTEx
rs4519744	ANAPC13	cis	Thyroid	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134313400-134321600	Weak transcription	Spleen	Spleen
2	chr3:134316600-134322200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:134317400-134322000	Enhancers	Fetal Brain Male	brain
4	chr3:134318000-134322400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:134318400-134321600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:134318400-134322200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:134319400-134321600	Enhancers	Brain Substantia Nigra	brain
8	chr3:134319400-134321600	Enhancers	Fetal Heart	heart
9	chr3:134319400-134322400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:134319600-134321600	Bivalent Enhancer	Fetal Stomach	stomach
11	chr3:134319600-134334600	Weak transcription	Aorta	Aorta
12	chr3:134319800-134321600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:134319800-134321800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:134319800-134353800	Weak transcription	Left Ventricle	heart
15	chr3:134320000-134321600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:134320000-134321600	Enhancers	Fetal Intestine Small	intestine
17	chr3:134320000-134321600	Enhancers	Fetal Lung	lung
18	chr3:134320000-134324600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:134320000-134324800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:134320200-134321800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:134320200-134321800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:134320200-134321800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:134320200-134321800	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:134320200-134321800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:134320200-134322000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:134320200-134325400	Weak transcription	Adipose Nuclei	Adipose
27	chr3:134320400-134321600	Enhancers	Brain Anterior Caudate	brain
28	chr3:134320400-134321800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:134320400-134321800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:134320400-134322000	Enhancers	Brain Hippocampus Middle	brain
31	chr3:134320400-134322400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:134320400-134338000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:134320600-134321600	Enhancers	Fetal Intestine Large	intestine
34	chr3:134320600-134321800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:134320600-134321800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:134320600-134321800	Bivalent Enhancer	Placenta	Placenta
37	chr3:134320600-134324400	Weak transcription	Primary B cells from cord blood	blood
38	chr3:134320800-134322800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:134321000-134321600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:134321000-134321600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr3:134321000-134321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:134321000-134322200	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:134321000-134324800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:134321200-134322000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:134321200-134322600	Weak transcription	Right Ventricle	heart
46	chr3:134321200-134323400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:134321200-134324000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:134321200-134335200	Weak transcription	Ovary	ovary
49	chr3:134321400-134321600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr3:134321400-134321600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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