Variant report

Variant	rs11840566
Chromosome Location	chr13:49227507-49227508
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17071994	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026581	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026582	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2209084	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57517713	0.83[ASN][1000 genomes]
rs57542351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60631683	0.83[ASN][1000 genomes]
rs6561472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7339332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074980	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74074988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74075000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7985015	0.92[ASN][1000 genomes]
rs7997045	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001963	0.90[ASN][1000 genomes]
rs9285169	0.95[ASN][1000 genomes]
rs9591186	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591188	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9595938	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9595940	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9595941	0.92[AMR][1000 genomes]
rs9595942	0.92[AMR][1000 genomes]
rs9595947	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9595952	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9595955	0.96[ASN][1000 genomes]
rs9595958	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49222600-49229400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:49226400-49227800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr13:49226600-49227600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:49226600-49227800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:49226600-49227800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr13:49226600-49228200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr13:49226800-49227600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:49226800-49227600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr13:49226800-49228000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:49227000-49227600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:49227000-49227600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr13:49227000-49227800	Enhancers	Primary B cells from cord blood	blood
13	chr13:49227000-49227800	Enhancers	Fetal Thymus	thymus
14	chr13:49227000-49228000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr13:49227000-49228400	Flanking Active TSS	Dnd41	blood
16	chr13:49227000-49229000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:49227000-49229000	Enhancers	Fetal Lung	lung
18	chr13:49227200-49227600	Enhancers	Fetal Intestine Large	intestine
19	chr13:49227200-49227600	Enhancers	Fetal Muscle Leg	muscle
20	chr13:49227200-49227600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr13:49227200-49227800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr13:49227200-49227800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr13:49227200-49227800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:49227200-49227800	Enhancers	Duodenum Mucosa	Duodenum
25	chr13:49227200-49227800	Enhancers	Placenta	Placenta
26	chr13:49227200-49227800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr13:49227200-49228000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr13:49227200-49228000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:49227200-49228200	Enhancers	Primary B cells from peripheral blood	blood
30	chr13:49227200-49228200	Enhancers	Fetal Intestine Small	intestine
31	chr13:49227200-49228200	Enhancers	Fetal Stomach	stomach
32	chr13:49227200-49228200	Enhancers	Small Intestine	intestine
33	chr13:49227200-49228600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr13:49227200-49230000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:49227400-49227600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:49227400-49227600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:49227400-49227600	Flanking Active TSS	Fetal Brain Male	brain
38	chr13:49227400-49227600	Enhancers	GM12878-XiMat	blood
39	chr13:49227400-49227800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr13:49227400-49227800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:49227400-49227800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr13:49227400-49227800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr13:49227400-49227800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr13:49227400-49227800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr13:49227400-49227800	Enhancers	Adipose Nuclei	Adipose
46	chr13:49227400-49227800	Enhancers	Fetal Kidney	kidney
47	chr13:49227400-49228000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr13:49227400-49228000	Enhancers	Stomach Mucosa	stomach
49	chr13:49227400-49228200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:49227400-49228200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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