Variant report

Variant	rs503918
Chromosome Location	chr11:58691355-58691356
allele	G/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	BACH1	chr11:58690792-58691378	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr11:58690739-58691367	H1-hESC	embryonic stem cell:	n/a	chr11:58691221-58691230 chr11:58691223-58691233
3	FOS	chr11:58690786-58691389	MCF10A-Er-Src	breast:	n/a	chr11:58691223-58691230 chr11:58691222-58691232 chr11:58691223-58691231 chr11:58691223-58691231
4	FOS	chr11:58690947-58691379	MCF10A-Er-Src	breast:	n/a	chr11:58691223-58691230 chr11:58691222-58691232 chr11:58691223-58691231 chr11:58691223-58691231
5	FOS	chr11:58690848-58691389	MCF10A-Er-Src	breast:	n/a	chr11:58691223-58691230 chr11:58691222-58691232 chr11:58691223-58691231 chr11:58691223-58691231
6	FOXA2	chr11:58691355-58691683	A549	lung:	n/a	n/a

Variant related genes	Relation type
GLYATL1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1788524	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1788538	0.85[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	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs481247	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs486950	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs487309	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[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	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs489732	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs494149	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs500462	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs503591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513877	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs517039	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs517387	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs522376	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[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	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs541258	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs544800	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs552591	0.82[CEU][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs565355	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs573322	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs577190	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs578396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578610	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6591500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58686200-58692600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:58687200-58694800	Enhancers	Fetal Intestine Large	intestine
3	chr11:58687200-58694800	Enhancers	Fetal Intestine Small	intestine
4	chr11:58689600-58694800	Weak transcription	Esophagus	oesophagus
5	chr11:58690000-58691800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:58690400-58693400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:58690600-58691400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:58690600-58691400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:58690600-58691600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:58690600-58692000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:58690600-58692000	Enhancers	Liver	Liver
12	chr11:58690600-58692600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr11:58690600-58694000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:58690800-58691400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr11:58690800-58691400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:58691000-58691400	Enhancers	Primary B cells from cord blood	blood
17	chr11:58691000-58691600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:58691000-58691600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr11:58691000-58692200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr11:58691000-58694400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:58691000-58695000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:58691000-58695200	Weak transcription	Stomach Mucosa	stomach
23	chr11:58691200-58691400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr11:58691200-58691400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:58691200-58691400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:58691200-58691400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:58691200-58691400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr11:58691200-58691600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr11:58691200-58691800	Enhancers	HMEC	breast
30	chr11:58691200-58692000	Weak transcription	Fetal Kidney	kidney
31	chr11:58691200-58692200	Enhancers	NHEK	skin
32	chr11:58691200-58692400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr11:58691200-58692400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr11:58691200-58692600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr11:58691200-58692600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr11:58691200-58693400	Weak transcription	NH-A	brain
37	chr11:58691200-58693600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:58691200-58693800	Weak transcription	Osteobl	bone
39	chr11:58691200-58694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:58691200-58694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:58691200-58694000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:58691200-58694400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:58691200-58694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:58691200-58694600	Weak transcription	Fetal Thymus	thymus
45	chr11:58691200-58694600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr11:58691200-58694600	Weak transcription	Thymus	Thymus
47	chr11:58691200-58694800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:58691200-58694800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:58691200-58694800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:58691200-58694800	Weak transcription	Duodenum Mucosa	Duodenum

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