Variant report

Variant	rs9535796
Chromosome Location	chr13:52512268-52512269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1051332	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1061472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1924608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924619	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1998611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2031992	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2282057	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296246	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2408510	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3825526	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7139967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140038	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7328751	0.83[ASN][1000 genomes]
rs752569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754609	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs928169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316562	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs942463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526812	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526814	0.85[CHB][hapmap]
rs9535792	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535793	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535795	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563078	0.81[JPT][hapmap]
rs9568677	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9591439	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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

No data

Chromatin state (count:75 , 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	chr13:52495400-52512600	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:52501600-52532400	Strong transcription	HepG2	liver
12	chr13:52502600-52514800	Weak transcription	HSMMtube	muscle
13	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
15	chr13:52504000-52515000	Weak transcription	K562	blood
16	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
19	chr13:52505600-52531800	Strong transcription	Liver	Liver
20	chr13:52505800-52513600	Strong transcription	Brain Germinal Matrix	brain
21	chr13:52505800-52513800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr13:52505800-52514000	Strong transcription	Fetal Stomach	stomach
23	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
24	chr13:52506000-52513400	Strong transcription	Left Ventricle	heart
25	chr13:52506000-52513400	Strong transcription	Ovary	ovary
26	chr13:52506000-52517200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
28	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:52507000-52517200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr13:52507200-52513400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr13:52507400-52517400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:52507400-52518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:52507800-52513400	Strong transcription	Pancreas	Pancrea
35	chr13:52508000-52512800	Strong transcription	Fetal Brain Female	brain
36	chr13:52508000-52514000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:52508200-52513400	Strong transcription	Brain Hippocampus Middle	brain
39	chr13:52508400-52513200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr13:52509000-52518200	Weak transcription	Esophagus	oesophagus
41	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
43	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr13:52509600-52518600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr13:52509800-52514800	Weak transcription	Brain Anterior Caudate	brain
47	chr13:52509800-52515600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
49	chr13:52510000-52518600	Weak transcription	Spleen	Spleen
50	chr13:52510200-52514800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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