Variant report

Variant	rs2147363
Chromosome Location	chr13:52542796-52542797
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	chr13:52538366..52539879-chr13:52542214..52544813,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1004576	0.83[CEU][hapmap]
rs1801243	0.82[CHD][hapmap]
rs1801244	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1886538	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2147359	0.82[EUR][1000 genomes]
rs2147360	0.82[EUR][1000 genomes]
rs2181891	0.82[CHD][hapmap]
rs2408554	0.83[CEU][hapmap]
rs3742288	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3783240	0.88[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825527	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4941720	0.82[EUR][1000 genomes]
rs732071	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7321435	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs747781	0.82[CHD][hapmap]
rs7998770	0.83[CEU][hapmap]
rs7999812	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9526817	0.82[EUR][1000 genomes]
rs9535812	0.82[CHD][hapmap]
rs9535816	0.82[EUR][1000 genomes]
rs9535821	0.81[EUR][1000 genomes]
rs9535824	0.82[EUR][1000 genomes]
rs9535873	0.83[CEU][hapmap]
rs9568682	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs9568684	0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2147363	NCRNA00282	cis	cerebellum	SCAN
rs2147363	CKAP2	cis	parietal	SCAN
rs2147363	NEK5	cis	cerebellum	SCAN
rs2147363	ATP7B	cis	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
4	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
7	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
8	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
13	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
15	chr13:52525400-52553000	Weak transcription	Ovary	ovary
16	chr13:52528000-52543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:52528400-52544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
19	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr13:52530400-52549000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:52530600-52550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:52530800-52544600	Weak transcription	Pancreas	Pancrea
23	chr13:52530800-52553000	Weak transcription	Fetal Lung	lung
24	chr13:52532800-52548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:52532800-52553000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr13:52533200-52544600	Strong transcription	HepG2	liver
27	chr13:52534400-52544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr13:52534600-52546000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr13:52536200-52548400	Weak transcription	Colonic Mucosa	Colon
31	chr13:52536600-52545000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr13:52537000-52552800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr13:52538600-52544600	Strong transcription	Liver	Liver
34	chr13:52539200-52543600	Strong transcription	Fetal Stomach	stomach
35	chr13:52539600-52542800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr13:52539800-52545800	Weak transcription	Right Ventricle	heart
37	chr13:52540000-52554600	Weak transcription	HSMMtube	muscle
38	chr13:52540400-52542800	Enhancers	Primary T cells from cord blood	blood
39	chr13:52540400-52542800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr13:52540400-52545200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr13:52540400-52550400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr13:52541000-52553000	Weak transcription	Left Ventricle	heart
43	chr13:52541200-52543000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr13:52541400-52554800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:52541600-52544800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:52541600-52545000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr13:52541800-52544800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:52541800-52546000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr13:52541800-52546800	Enhancers	Stomach Mucosa	stomach
50	chr13:52541800-52553000	Weak transcription	Right Atrium	heart

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