Variant report

Variant	rs9526814
Chromosome Location	chr13:52539526-52539527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52534596..52536484-chr13:52537213..52539765,2	K562	blood:
2	chr13:52538366..52539879-chr13:52542214..52544813,2	K562	blood:
3	chr13:52538268..52540187-chr13:52546214..52549057,2	K562	blood:

Variant related genes	Relation type
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051332	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1061472	0.85[CHB][hapmap]
rs1801243	0.85[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1801244	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1801249	0.85[CHB][hapmap]
rs1924608	0.85[CHB][hapmap]
rs1924609	0.85[CHB][hapmap]
rs1951922	0.82[EUR][1000 genomes]
rs1998611	0.85[CHB][hapmap]
rs2031992	0.85[CHB][hapmap]
rs2104353	0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2181891	0.85[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2282058	0.84[CHB][hapmap]
rs2296246	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3742288	0.89[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3783240	0.85[CHB][hapmap]
rs3783241	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825526	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3825527	0.89[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4943044	0.85[CHB][hapmap]
rs4943045	0.85[CHB][hapmap]
rs4943046	0.85[CHB][hapmap]
rs4943048	0.85[CHB][hapmap]
rs7139967	0.85[CHB][hapmap]
rs7321445	0.85[CHB][hapmap]
rs7321909	0.85[CHB][hapmap]
rs732774	0.85[CHB][hapmap]
rs747781	0.85[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs750290	0.83[EUR][1000 genomes]
rs752569	0.85[CHB][hapmap]
rs752570	0.95[EUR][1000 genomes]
rs754610	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7999812	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs942463	0.85[CHB][hapmap]
rs9526811	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9526812	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9535796	0.85[CHB][hapmap]
rs9535797	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535812	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9563078	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs9568677	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9568681	0.83[EUR][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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9526814	NCRNA00282	cis	cerebellum	SCAN
rs9526814	CKAP2	cis	cerebellum	SCAN
rs9526814	ALG11	cis	Artery Tibial	GTEx
rs9526814	CKAP2	cis	multi-tissue	Pritchard
rs9526814	LOC440138	cis	multi-tissue	Pritchard
rs9526814	CKAP2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
3	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
6	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
9	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
10	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
16	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
18	chr13:52525400-52553000	Weak transcription	Ovary	ovary
19	chr13:52528000-52543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:52528400-52540800	Weak transcription	Lung	lung
21	chr13:52528400-52544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr13:52528800-52542200	Weak transcription	Fetal Heart	heart
23	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
24	chr13:52529800-52541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr13:52530200-52542000	Weak transcription	Brain Germinal Matrix	brain
26	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:52530400-52541600	Weak transcription	Fetal Thymus	thymus
28	chr13:52530400-52549000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:52530600-52550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:52530800-52539800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr13:52530800-52544600	Weak transcription	Pancreas	Pancrea
32	chr13:52530800-52553000	Weak transcription	Fetal Lung	lung
33	chr13:52531000-52540400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr13:52532400-52541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:52532800-52539600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr13:52532800-52539800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:52532800-52542000	Weak transcription	Brain Anterior Caudate	brain
38	chr13:52532800-52548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:52532800-52553000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr13:52533200-52544600	Strong transcription	HepG2	liver
41	chr13:52534200-52541600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:52534400-52544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:52534600-52542000	Weak transcription	Gastric	stomach
45	chr13:52534600-52546000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:52536000-52539600	Weak transcription	Fetal Muscle Leg	muscle
47	chr13:52536200-52548400	Weak transcription	Colonic Mucosa	Colon
48	chr13:52536600-52539600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr13:52536600-52545000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:52537000-52539600	Weak transcription	Duodenum Mucosa	Duodenum

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