Variant report

Variant	rs578396
Chromosome Location	chr11:58692953-58692954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1788524	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1788538	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1788550	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs472554	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs474253	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs481247	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs486950	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs487309	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs487920	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs488737	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs489732	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs494149	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs500462	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs503591	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503918	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513877	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs517039	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs517387	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs522376	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs530180	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs531578	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534890	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs538678	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs541258	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs544800	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs552591	0.92[ASN][1000 genomes]
rs565355	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs573322	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs577190	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs578610	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6591500	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription 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	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3502182	chr11:58668199-58731237	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3502181	chr11:58668236-58731215	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3478019	chr11:58668282-58731214	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3478030	chr11:58668282-58731214	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3502183	chr11:58668353-58731177	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58687200-58694800	Enhancers	Fetal Intestine Large	intestine
2	chr11:58687200-58694800	Enhancers	Fetal Intestine Small	intestine
3	chr11:58689600-58694800	Weak transcription	Esophagus	oesophagus
4	chr11:58690400-58693400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:58690600-58694000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:58691000-58694400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:58691000-58695000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr11:58691000-58695200	Weak transcription	Stomach Mucosa	stomach
9	chr11:58691200-58693400	Weak transcription	NH-A	brain
10	chr11:58691200-58693600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:58691200-58693800	Weak transcription	Osteobl	bone
12	chr11:58691200-58694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:58691200-58694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:58691200-58694000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:58691200-58694400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:58691200-58694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:58691200-58694600	Weak transcription	Fetal Thymus	thymus
18	chr11:58691200-58694600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:58691200-58694600	Weak transcription	Thymus	Thymus
20	chr11:58691200-58694800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:58691200-58694800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr11:58691200-58694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:58691200-58694800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:58691200-58695000	Weak transcription	Brain Anterior Caudate	brain
25	chr11:58691200-58695200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:58691200-58695200	Weak transcription	Colonic Mucosa	Colon
27	chr11:58691200-58695200	Weak transcription	Fetal Lung	lung
28	chr11:58691400-58693600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:58691400-58693600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:58691400-58693800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:58691400-58694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:58691400-58694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:58691400-58694800	Weak transcription	Primary B cells from cord blood	blood
34	chr11:58691600-58694600	Weak transcription	Pancreas	Pancrea
35	chr11:58691600-58694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:58691600-58695000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:58691600-58695800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:58691800-58694800	Weak transcription	HMEC	breast
39	chr11:58692200-58693200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr11:58692200-58694600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:58692200-58694800	Weak transcription	NHEK	skin
42	chr11:58692200-58695200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:58692400-58694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:58692400-58694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:58692400-58695200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:58692600-58693800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:58692600-58693800	Weak transcription	Fetal Kidney	kidney
48	chr11:58692600-58694000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:58692600-58694000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:58692600-58694200	Weak transcription	H1 Cell Line	embryonic stem cell

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