Variant report

Variant	rs9526979
Chromosome Location	chr13:53258289-53258290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53225756..53229849-chr13:53255678..53259863,4	K562	blood:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1057478	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4284531	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959657	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526975	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9526982	0.82[AFR][1000 genomes]
rs9536185	0.89[ASN][1000 genomes]
rs9536190	0.89[ASN][1000 genomes]
rs9536199	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9536204	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536220	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9536236	0.84[EUR][1000 genomes]
rs9536242	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv900088	chr13:53250839-53274936	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9526979	CKAP2	cis	Nerve Tibial	GTEx
rs9526979	CKAP2	cis	Thyroid	GTEx
rs9526979	CKAP2	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53227800-53260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53229000-53276600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:53229200-53268000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr13:53230200-53263600	Weak transcription	Stomach Mucosa	stomach
5	chr13:53230400-53266400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:53230600-53266400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr13:53230800-53277400	Weak transcription	Gastric	stomach
8	chr13:53231200-53262400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:53231800-53266400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr13:53235200-53276000	Weak transcription	Right Ventricle	heart
11	chr13:53237200-53261800	Weak transcription	Fetal Brain Male	brain
12	chr13:53239200-53265600	Weak transcription	Brain Angular Gyrus	brain
13	chr13:53240600-53264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:53240600-53275800	Weak transcription	K562	blood
15	chr13:53242800-53278600	Weak transcription	Psoas Muscle	Psoas
16	chr13:53243200-53259000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr13:53245400-53263800	Strong transcription	Dnd41	blood
18	chr13:53245600-53263600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr13:53248400-53265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:53248600-53263400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr13:53248600-53265200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr13:53249000-53263400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:53249000-53263400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr13:53249000-53263600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr13:53249000-53266400	Strong transcription	Liver	Liver
26	chr13:53249000-53266400	Strong transcription	Fetal Intestine Large	intestine
27	chr13:53249000-53266600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:53249000-53267400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:53249200-53259400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:53249200-53261000	Strong transcription	Adipose Nuclei	Adipose
31	chr13:53249200-53263400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:53249200-53265200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:53249600-53262800	Strong transcription	Fetal Thymus	thymus
34	chr13:53249800-53266000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr13:53250000-53263800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr13:53250000-53265000	Weak transcription	Hela-S3	cervix
37	chr13:53250400-53262400	Strong transcription	Placenta	Placenta
38	chr13:53250400-53263400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:53250600-53260000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:53250600-53260600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr13:53250600-53263400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:53250800-53266600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:53251000-53263600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr13:53251400-53267400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr13:53252400-53263000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:53253200-53260600	Strong transcription	HSMMtube	muscle
47	chr13:53253800-53263800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:53254200-53259200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:53254200-53275800	Weak transcription	Fetal Heart	heart
50	chr13:53254400-53260400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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