Variant report

Variant	rs11927539
Chromosome Location	chr3:134319448-134319449
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134314944..134317745-chr3:134318153..134321546,4	K562	blood:
2	chr3:134319269..134320640-chr3:134359487..134360406,9	MCF-7	breast:
3	chr3:134317378..134319785-chr3:134321623..134324001,2	K562	blood:
4	chr3:134319433..134320274-chr3:134473723..134474504,4	MCF-7	breast:
5	chr3:134319400..134320351-chr3:135222419..135223319,2	MCF-7	breast:
6	chr3:134319413..134320198-chr3:134473635..134474163,2	K562	blood:
7	chr3:134319359..134320307-chr3:134395413..134396701,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KY-3	chr3:134318765-134320752	NONHSAT092252

No data

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	0.84[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]
rs11927540	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637301	1.00[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	0.91[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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534030	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880378	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880379	0.89[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	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2293293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293294	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888670	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4074521	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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245904	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245905	0.89[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	0.91[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]
rs4519744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535271	0.86[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	0.94[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	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4955525	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955534	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955542	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955544	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955545	0.88[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	0.96[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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779326	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782563	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	0.97[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	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7611611	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623567	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633868	0.89[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	1.00[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	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9809344	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824185	0.98[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	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838467	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838621	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838889	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839705	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9841371	0.98[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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9851441	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9857242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857995	0.98[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	0.87[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
rs11927539	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs11927539	ANAPC13	cis	Nerve Tibial	GTEx
rs11927539	CEP63	cis	Esophagus Muscularis	GTEx
rs11927539	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs11927539	ANAPC13	cis	Thyroid	GTEx
rs11927539	ANAPC13	cis	Artery Tibial	GTEx
rs11927539	CEP63	cis	Artery Tibial	GTEx
rs11927539	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs11927539	CEP63	cis	Esophagus Mucosa	GTEx
rs11927539	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs11927539	ANAPC13	cis	multi-tissue	Pritchard
rs11927539	ANAPC13	cis	Artery Aorta	GTEx
rs11927539	CEP63	cis	lung	GTEx
rs11927539	ANAPC13	cis	Muscle Skeletal	GTEx
rs11927539	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs11927539	ANAPC13	cis	Stomach	GTEx
rs11927539	ANAPC13	cis	lung	GTEx
rs11927539	ANAPC13	cis	Esophagus Muscularis	GTEx
rs11927539	ANAPC13	cis	Esophagus Mucosa	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134311600-134320400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:134313400-134321600	Weak transcription	Spleen	Spleen
3	chr3:134316600-134322200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:134317200-134320000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:134317400-134319800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:134317400-134322000	Enhancers	Fetal Brain Male	brain
7	chr3:134317600-134319800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:134317800-134319600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:134317800-134319800	Enhancers	Fetal Brain Female	brain
10	chr3:134317800-134320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:134318000-134319600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:134318000-134322400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:134318200-134319600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:134318200-134319600	Weak transcription	Brain Germinal Matrix	brain
15	chr3:134318200-134319600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:134318400-134319600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:134318400-134321600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:134318400-134322200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:134318800-134319600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:134319200-134319600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:134319200-134319600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:134319200-134319600	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:134319200-134319600	Enhancers	Brain Hippocampus Middle	brain
24	chr3:134319200-134319800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:134319200-134319800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:134319200-134320600	Enhancers	HMEC	breast
27	chr3:134319400-134319600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
28	chr3:134319400-134319600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:134319400-134319600	Enhancers	Aorta	Aorta
30	chr3:134319400-134319600	Bivalent/Poised TSS	NHLF	lung
31	chr3:134319400-134319600	Bivalent Enhancer	Osteobl	bone
32	chr3:134319400-134319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:134319400-134319800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:134319400-134320000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:134319400-134320200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr3:134319400-134320600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:134319400-134320600	Enhancers	NHEK	skin
38	chr3:134319400-134321000	Enhancers	Fetal Muscle Leg	muscle
39	chr3:134319400-134321400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:134319400-134321400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:134319400-134321600	Enhancers	Brain Substantia Nigra	brain
42	chr3:134319400-134321600	Enhancers	Fetal Heart	heart
43	chr3:134319400-134322400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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