Variant report

Variant	rs57549228
Chromosome Location	chr11:58694747-58694748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:58694591-58696288	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOXA1	chr11:58694663-58695208	T-47D	breast:	n/a	n/a
3	TAF1	chr11:58694671-58695628	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr11:58694741-58695236	T-47D	breast:	n/a	n/a
5	SP1	chr11:58694715-58695473	H1-hESC	embryonic stem cell:	n/a	chr11:58695087-58695098 chr11:58695027-58695039 chr11:58695027-58695039 chr11:58695028-58695037 chr11:58695029-58695038

Variant related genes	Relation type
GLYATL1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1783530	1.00[AMR][1000 genomes]
rs1943141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2187267	1.00[EUR][1000 genomes]
rs473548	1.00[EUR][1000 genomes]
rs476776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4939242	1.00[EUR][1000 genomes]
rs506360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs508359	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs512676	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs518154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524526	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs524585	1.00[EUR][1000 genomes]
rs524821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs531424	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs531497	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs540242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs541312	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs542363	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs560837	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56092931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56208934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs562744	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs572417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57426705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58476503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58772644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs666228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs693161	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs693371	1.00[EUR][1000 genomes]
rs7933301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7946085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7946855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:58 , 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	chr11:58691000-58695000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:58691000-58695200	Weak transcription	Stomach Mucosa	stomach
6	chr11:58691200-58694800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:58691200-58694800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr11:58691200-58694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:58691200-58694800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:58691200-58695000	Weak transcription	Brain Anterior Caudate	brain
11	chr11:58691200-58695200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:58691200-58695200	Weak transcription	Colonic Mucosa	Colon
13	chr11:58691200-58695200	Weak transcription	Fetal Lung	lung
14	chr11:58691400-58694800	Weak transcription	Primary B cells from cord blood	blood
15	chr11:58691600-58694800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:58691600-58695000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:58691600-58695800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:58691800-58694800	Weak transcription	HMEC	breast
19	chr11:58692200-58694800	Weak transcription	NHEK	skin
20	chr11:58692200-58695200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:58692400-58695200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:58692600-58695000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:58692600-58695000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:58692600-58695000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:58693400-58694800	Enhancers	HepG2	liver
26	chr11:58693400-58695800	Enhancers	NH-A	brain
27	chr11:58693600-58695000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:58693600-58695800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:58693800-58695000	Enhancers	Fetal Kidney	kidney
30	chr11:58693800-58695000	Enhancers	Osteobl	bone
31	chr11:58693800-58695800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr11:58694000-58695000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:58694000-58695200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr11:58694000-58695800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:58694000-58696000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:58694200-58694800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr11:58694400-58694800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr11:58694400-58694800	Enhancers	Primary hematopoietic stem cells	blood
39	chr11:58694400-58694800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr11:58694400-58695000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:58694400-58695400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:58694400-58696200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:58694600-58694800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:58694600-58694800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr11:58694600-58694800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:58694600-58694800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:58694600-58694800	Enhancers	Fetal Brain Female	brain
48	chr11:58694600-58694800	Enhancers	Pancreas	Pancrea
49	chr11:58694600-58694800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr11:58694600-58694800	Enhancers	Rectal Mucosa Donor 31	rectum

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