Variant report

Variant	rs12223829
Chromosome Location	chr11:74546064-74546065
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10899043	0.84[ASN][1000 genomes]
rs11236255	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1125609	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs113187	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11827626	0.96[ASN][1000 genomes]
rs1282668	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1282675	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282677	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1315265	0.94[ASN][1000 genomes]
rs1315299	0.93[ASN][1000 genomes]
rs1821352	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866562	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2436762	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510692	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132738	0.84[ASN][1000 genomes]
rs3132908	0.84[ASN][1000 genomes]
rs474431	0.85[ASN][1000 genomes]
rs474445	0.97[ASN][1000 genomes]
rs474970	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs476040	0.84[ASN][1000 genomes]
rs483271	0.95[ASN][1000 genomes]
rs487207	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487226	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs491826	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs493889	0.95[ASN][1000 genomes]
rs496698	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs498527	0.85[ASN][1000 genomes]
rs500827	0.98[ASN][1000 genomes]
rs503855	0.96[ASN][1000 genomes]
rs503994	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs504970	0.85[ASN][1000 genomes]
rs507247	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs507620	0.85[ASN][1000 genomes]
rs512782	0.94[ASN][1000 genomes]
rs513157	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs514534	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515429	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs516287	0.95[ASN][1000 genomes]
rs517035	0.85[ASN][1000 genomes]
rs517666	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517939	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs524187	0.84[ASN][1000 genomes]
rs525802	0.85[ASN][1000 genomes]
rs527099	0.85[ASN][1000 genomes]
rs527661	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs528800	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs529186	0.85[ASN][1000 genomes]
rs532952	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs533220	0.80[ASN][1000 genomes]
rs534595	0.96[ASN][1000 genomes]
rs535705	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs535794	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs536823	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs544852	0.85[ASN][1000 genomes]
rs544891	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs545202	0.86[ASN][1000 genomes]
rs545304	0.86[ASN][1000 genomes]
rs548106	0.84[ASN][1000 genomes]
rs550909	0.84[ASN][1000 genomes]
rs556908	0.85[ASN][1000 genomes]
rs556916	0.85[ASN][1000 genomes]
rs557804	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs558303	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs559211	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563473	0.85[ASN][1000 genomes]
rs564229	0.85[ASN][1000 genomes]
rs571250	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs571437	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs575064	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs575886	0.86[ASN][1000 genomes]
rs576661	0.84[ASN][1000 genomes]
rs578477	0.95[ASN][1000 genomes]
rs579581	0.95[ASN][1000 genomes]
rs580042	0.85[ASN][1000 genomes]
rs580299	0.85[ASN][1000 genomes]
rs580541	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592045	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605954	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633824	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs650130	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs655488	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs662062	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs670246	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs673731	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693212	0.98[ASN][1000 genomes]
rs7121530	0.81[EUR][1000 genomes];0.98[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	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
4	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74533600-74546200	Weak transcription	Aorta	Aorta
3	chr11:74533600-74546200	Weak transcription	Psoas Muscle	Psoas
4	chr11:74533600-74546400	Weak transcription	Right Ventricle	heart
5	chr11:74533800-74553200	Weak transcription	Fetal Heart	heart
6	chr11:74536000-74546400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:74538200-74546400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:74538400-74546200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:74538400-74546200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:74538400-74546400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:74538400-74546400	Weak transcription	Esophagus	oesophagus
12	chr11:74538400-74546400	Weak transcription	HSMMtube	muscle
13	chr11:74538400-74546400	Weak transcription	K562	blood
14	chr11:74538400-74546600	Weak transcription	NHLF	lung
15	chr11:74538400-74553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:74538400-74559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:74538400-74560000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:74538600-74546200	Weak transcription	A549	lung
19	chr11:74538600-74546400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:74538600-74546400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:74538600-74546400	Weak transcription	Hela-S3	cervix
22	chr11:74538600-74546600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:74538600-74554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:74539200-74546600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:74539200-74557200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:74540000-74548600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:74541000-74550000	Strong transcription	Primary B cells from cord blood	blood
28	chr11:74541600-74549800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:74541600-74551400	Strong transcription	Primary T cells from cord blood	blood
30	chr11:74541800-74556400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:74542400-74546200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:74542400-74549400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:74543200-74546600	Weak transcription	Fetal Brain Male	brain
34	chr11:74543600-74548400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:74543800-74549800	Strong transcription	Liver	Liver
36	chr11:74543800-74550000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:74543800-74550800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:74544000-74549800	Strong transcription	Adipose Nuclei	Adipose
40	chr11:74544000-74550600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:74544000-74557400	Strong transcription	Dnd41	blood
42	chr11:74544000-74557600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:74544200-74548800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:74544200-74549600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:74544200-74549800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:74544200-74550200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr11:74544200-74550400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:74544200-74557200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:74544200-74558400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum

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