Variant report

Variant	rs2296246
Chromosome Location	chr13:52520704-52520705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1051332	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1061472	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1801243	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1801244	0.85[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1801249	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1924608	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1924609	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1951922	0.81[EUR][1000 genomes]
rs1998611	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2031992	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181891	0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2282058	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3742288	0.85[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3783240	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3783241	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3825526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825527	0.85[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4943044	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943045	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943046	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943048	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7139967	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7321445	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7321909	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs732774	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs747781	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs750290	0.82[EUR][1000 genomes]
rs752569	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs752570	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7999812	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs942463	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526811	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526814	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]
rs9535796	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9535797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535812	0.81[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs9563078	0.96[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568681	0.82[EUR][1000 genomes]
rs9591438	0.88[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	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
rs2296246	CKAP2	cis	cerebellum	SCAN
rs2296246	NCRNA00282	cis	cerebellum	SCAN
rs2296246	ALG11	cis	Artery Tibial	GTEx
rs2296246	CKAP2	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
4	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
6	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:52501600-52532400	Strong transcription	HepG2	liver
9	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
10	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
13	chr13:52505600-52531800	Strong transcription	Liver	Liver
14	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
15	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
16	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
21	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
24	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
26	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
27	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:52514600-52521000	Strong transcription	Fetal Muscle Leg	muscle
30	chr13:52514800-52520800	Strong transcription	Brain Anterior Caudate	brain
31	chr13:52516000-52531800	Weak transcription	Fetal Kidney	kidney
32	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:52516200-52524800	Weak transcription	Fetal Heart	heart
34	chr13:52516600-52520800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:52516800-52522000	Weak transcription	K562	blood
37	chr13:52516800-52529200	Weak transcription	Pancreas	Pancrea
38	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr13:52518000-52520800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr13:52518400-52529200	Weak transcription	Colonic Mucosa	Colon
41	chr13:52518600-52520800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:52518600-52528600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr13:52518600-52528600	Weak transcription	Stomach Mucosa	stomach
44	chr13:52518800-52523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr13:52518800-52524200	Weak transcription	Lung	lung
46	chr13:52518800-52527600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:52519000-52523600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:52519000-52523600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr13:52519200-52520800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr13:52519200-52523800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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