Variant report

Variant	rs9526950
Chromosome Location	chr13:53174463-53174464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53028617..53031103-chr13:53172840..53175725,3	MCF-7	breast:
2	chr12:93771675..93772184-chr13:53174171..53174759,2	NB4	blood:
3	chr13:53172771..53175608-chr13:53190178..53193759,4	MCF-7	breast:
4	chr13:53173175..53175683-chr13:53225993..53228450,3	MCF-7	breast:
5	chr13:53023875..53025638-chr13:53174219..53175747,2	MCF-7	breast:
6	chr10:131908141..131909040-chr13:53174069..53174686,2	Hela-S3	cervix:
7	chr13:53174054..53174958-chr19:10443932..10444611,2	NB4	blood:

Variant related genes	Relation type
ENSG00000136108	Chromatin interaction
ENSG00000136100	Chromatin interaction
ENSG00000161847	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000139675	Chromatin interaction
ENSG00000250299	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1057478	0.84[ASN][1000 genomes]
rs4284531	0.82[ASN][1000 genomes]
rs61958118	0.81[EUR][1000 genomes]
rs61959657	0.81[ASN][1000 genomes]
rs9536185	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9536190	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9536199	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9536204	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9536220	0.84[ASN][1000 genomes]
rs9536242	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
5	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	14 gene(s)	inside rSNPs	diseases
7	nsv1038132	chr13:53057359-53190994	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2760295	chr13:53071152-53178504	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv900087	chr13:53119704-53208030	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	esv13738	chr13:53159859-53177755	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
17	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
21	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	esv3335654	chr13:53173751-53175599	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9526950	CKAP2	cis	Nerve Tibial	GTEx
rs9526950	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9526950	CKAP2	cis	Artery Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53173200-53174800	Active TSS	Brain Angular Gyrus	brain
2	chr13:53173200-53174800	Flanking Active TSS	HMEC	breast
3	chr13:53173400-53174800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr13:53173400-53175200	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr13:53173400-53175200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr13:53173400-53175400	Flanking Active TSS	HUVEC	blood vessel
7	chr13:53173600-53174800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:53173600-53174800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr13:53173600-53174800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:53173600-53174800	Active TSS	Aorta	Aorta
11	chr13:53173600-53174800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:53173600-53174800	Active TSS	Fetal Intestine Large	intestine
13	chr13:53173600-53174800	Active TSS	Ovary	ovary
14	chr13:53173600-53175000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr13:53173600-53175000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:53173600-53175000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:53173600-53175000	Active TSS	Fetal Muscle Trunk	muscle
18	chr13:53173600-53175200	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr13:53173600-53175200	Active TSS	Stomach Smooth Muscle	stomach
20	chr13:53173600-53175200	Active TSS	NHDF-Ad	bronchial
21	chr13:53173800-53174600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:53173800-53174600	Enhancers	Gastric	stomach
23	chr13:53173800-53174600	Active TSS	Left Ventricle	heart
24	chr13:53173800-53174600	Active TSS	Placenta Amnion	Placenta Amnion
25	chr13:53173800-53174600	Active TSS	Rectal Smooth Muscle	rectum
26	chr13:53173800-53174600	Bivalent/Poised TSS	NHLF	lung
27	chr13:53173800-53174800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr13:53173800-53174800	Active TSS	H9 Cell Line	embryonic stem cell
29	chr13:53173800-53174800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:53173800-53174800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:53173800-53174800	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr13:53173800-53174800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr13:53173800-53174800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr13:53173800-53174800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
35	chr13:53173800-53174800	Active TSS	Brain Anterior Caudate	brain
36	chr13:53173800-53174800	Active TSS	Brain Cingulate Gyrus	brain
37	chr13:53173800-53174800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
38	chr13:53173800-53174800	Active TSS	Colonic Mucosa	Colon
39	chr13:53173800-53174800	Active TSS	Colon Smooth Muscle	Colon
40	chr13:53173800-53174800	Active TSS	Fetal Intestine Small	intestine
41	chr13:53173800-53174800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr13:53173800-53174800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr13:53173800-53174800	Bivalent/Poised TSS	Thymus	Thymus
44	chr13:53173800-53175000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:53173800-53175000	Active TSS	Brain Hippocampus Middle	brain
46	chr13:53173800-53175000	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr13:53173800-53175000	Active TSS	Fetal Brain Female	brain
48	chr13:53173800-53175000	Active TSS	Fetal Lung	lung
49	chr13:53173800-53175000	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:53173800-53175000	Active TSS	HepG2	liver

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