Variant report

Variant	rs9526914
Chromosome Location	chr13:52976300-52976301
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52976129..52976672-chr13:53024355..53025202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1056335	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11148252	0.88[ASN][1000 genomes]
rs11618716	0.86[ASN][1000 genomes]
rs11620062	0.89[ASN][1000 genomes]
rs13431	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1815669	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803262	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803264	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886077	0.91[ASN][1000 genomes]
rs4286007	0.87[ASN][1000 genomes]
rs4884320	0.93[ASN][1000 genomes]
rs4884354	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4884452	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4885953	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886018	0.91[ASN][1000 genomes]
rs4886077	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61958050	0.94[ASN][1000 genomes]
rs6561665	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7323666	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7333451	0.90[ASN][1000 genomes]
rs7336679	0.90[ASN][1000 genomes]
rs7399631	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7985262	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7987115	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8001624	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379	0.90[ASN][1000 genomes]
rs9526913	0.95[ASN][1000 genomes]
rs9536046	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536048	0.98[ASN][1000 genomes]
rs9536052	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536069	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9568728	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9596643	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9596648	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9526914	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9526914	CKAP2	cis	Nerve Tibial	GTEx
rs9526914	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9526914	CKAP2	cis	Artery Tibial	GTEx
rs9526914	CKAP2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52946200-52979200	Weak transcription	A549	lung
2	chr13:52949800-52979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:52956200-52978200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:52967800-52978800	Weak transcription	NH-A	brain
5	chr13:52968200-52979600	Weak transcription	Gastric	stomach
6	chr13:52968400-52978600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr13:52968400-52978600	Weak transcription	NHDF-Ad	bronchial
8	chr13:52969000-52977600	Strong transcription	HSMM	muscle
9	chr13:52969600-52978600	Weak transcription	Fetal Brain Male	brain
10	chr13:52970000-52979200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:52970000-52979400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:52970200-52977200	Weak transcription	Adipose Nuclei	Adipose
13	chr13:52970200-52979400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:52970200-52979400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:52970400-52978200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:52971800-52979600	Weak transcription	Pancreas	Pancrea
17	chr13:52972000-52978600	Weak transcription	Right Ventricle	heart
18	chr13:52972000-52978600	Weak transcription	NHLF	lung
19	chr13:52972000-52979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:52972000-52979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:52972200-52977400	Weak transcription	HUVEC	blood vessel
22	chr13:52972200-52978200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:52972200-52978200	Weak transcription	Left Ventricle	heart
24	chr13:52972200-52978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:52972200-52978600	Weak transcription	NHEK	skin
26	chr13:52972200-52979200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:52972200-52979600	Weak transcription	Spleen	Spleen
28	chr13:52972400-52978400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:52972600-52977000	Weak transcription	HMEC	breast
30	chr13:52972600-52977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:52972600-52978200	Weak transcription	Lung	lung
32	chr13:52972600-52978400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:52972800-52977400	Weak transcription	Fetal Muscle Leg	muscle
34	chr13:52974000-52979400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:52974000-52979400	Weak transcription	Fetal Brain Female	brain
36	chr13:52974200-52978200	Weak transcription	Brain Hippocampus Middle	brain
37	chr13:52974400-52977200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:52974600-52978200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:52975000-52977200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:52975800-52976400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:52975800-52976800	Strong transcription	HSMMtube	muscle
42	chr13:52976000-52977000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:52976200-52978400	Weak transcription	Osteobl	bone

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