Variant report

Variant	rs530481
Chromosome Location	chr11:58690730-58690731
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	RAD21	chr11:58690712-58690964	HepG2	liver:	n/a	n/a
2	CTCF	chr11:58690660-58690810	HVMF	connective:	n/a	n/a
3	KAP1	chr11:58690728-58691180	U2OS	brain:	n/a	n/a
4	CTCF	chr11:58690720-58690870	GM12872	blood:	n/a	n/a
5	CTCF	chr11:58690547-58691196	HCT-116	colon:	n/a	n/a
6	CTCF	chr11:58690665-58691018	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr11:58690585-58690964	HepG2	liver:	n/a	n/a
8	FOXA1	chr11:58690618-58690985	T-47D	breast:	n/a	n/a
9	CTCF	chr11:58690620-58690770	AG09309	skin:	n/a	n/a
10	JUND	chr11:58690723-58691304	H1-hESC	embryonic stem cell:	n/a	chr11:58691223-58691230 chr11:58691222-58691232 chr11:58691223-58691231 chr11:58691223-58691231
11	SP1	chr11:58690632-58691230	H1-hESC	embryonic stem cell:	n/a	chr11:58691179-58691193 chr11:58691180-58691189 chr11:58691179-58691188 chr11:58691178-58691190
12	RAD21	chr11:58690590-58690990	SK-N-SH_RA	brain:	n/a	n/a
13	RAD21	chr11:58690694-58690956	HepG2	liver:	n/a	n/a
14	RAD21	chr11:58690649-58691043	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr11:58690676-58691027	K562	blood:	n/a	n/a
16	SMC3	chr11:58690714-58691016	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr11:58690636-58691039	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F4	chr11:58690610-58691223	MCF10A-Er-Src	breast:	n/a	n/a
19	EBF1	chr11:58690729-58691019	GM12878	blood:	n/a	n/a
20	CTCF	chr11:58690720-58690870	WERI-Rb-1	eye:	n/a	n/a
21	RAD21	chr11:58690619-58691128	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr11:58690610-58690948	H1-hESC	embryonic stem cell:	n/a	n/a
23	FOXA1	chr11:58690627-58690976	HepG2	liver:	n/a	n/a
24	SMC3	chr11:58690715-58691107	SK-N-SH	brain:	n/a	n/a
25	RAD21	chr11:58690710-58691011	IMR90	lung:	n/a	n/a
26	CTCF	chr11:58690668-58691023	HepG2	liver:	n/a	n/a
27	ZNF143	chr11:58690701-58691020	GM12878	blood:	n/a	n/a
28	CTCF	chr11:58690697-58690988	GM12878	blood:	n/a	n/a
29	RAD21	chr11:58690701-58690969	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr11:58690687-58690981	SK-N-SH_RA	brain:	n/a	n/a
31	SP1	chr11:58690686-58691162	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr11:58690700-58690850	HEK293	kidney:	n/a	n/a
33	JUND	chr11:58690728-58690980	K562	blood:	n/a	n/a
34	CTCF	chr11:58690720-58690870	WI-38	lung:	n/a	n/a
35	ZNF143	chr11:58690728-58690931	K562	blood:	n/a	n/a
36	CTCF	chr11:58690670-58691052	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr11:58690100-58691258	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr11:58690446-58691302	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr11:58690720-58690870	HAc	cerebellar:	n/a	n/a
40	CTCF	chr11:58690722-58691015	MCF-7	breast:	n/a	n/a
41	RAD21	chr11:58690698-58690923	GM12878	blood:	n/a	n/a
42	CTCF	chr11:58690729-58690954	K562	blood:	n/a	n/a
43	KAP1	chr11:58690562-58691257	HEK293	kidney:	n/a	chr11:58691221-58691230
44	RAD21	chr11:58690540-58691213	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr11:58690674-58690949	GM12878	blood:	n/a	n/a
46	CTCF	chr11:58690700-58690850	A549	lung:	n/a	n/a
47	CTCF	chr11:58690722-58690967	K562	blood:	n/a	n/a
48	CTCF	chr11:58690663-58691039	GM12878	blood:	n/a	n/a
49	CTCF	chr11:58690715-58690979	T-47D	breast:	n/a	n/a
50	CTCF	chr11:58690700-58690850	GM12870	blood:	n/a	n/a

Variant related genes	Relation type
GLYATL1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11229690	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229707	0.85[ASN][1000 genomes]
rs11603726	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1788552	0.81[ASN][1000 genomes]
rs1892866	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1938785	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1938787	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1938788	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2005121	0.87[ASN][1000 genomes]
rs2105736	0.85[ASN][1000 genomes]
rs2156322	0.81[ASN][1000 genomes]
rs474121	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478587	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478705	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480196	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs482751	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs483991	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486507	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs488446	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs489782	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs489846	0.88[ASN][1000 genomes]
rs501703	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs510360	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513677	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs516803	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs532318	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs533087	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs535218	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs538472	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs544687	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs546051	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs550864	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563370	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564335	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576790	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120597	0.87[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:49 , 50 per page) page: 1

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	chr11:58687400-58691200	Enhancers	Fetal Kidney	kidney
5	chr11:58687600-58690800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:58687800-58690800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr11:58689200-58691200	Enhancers	Colonic Mucosa	Colon
8	chr11:58689600-58694800	Weak transcription	Esophagus	oesophagus
9	chr11:58690000-58690800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr11:58690000-58690800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr11:58690000-58691800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:58690200-58691000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr11:58690400-58690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr11:58690400-58690800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr11:58690400-58690800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:58690400-58690800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:58690400-58690800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:58690400-58690800	Enhancers	NHEK	skin
19	chr11:58690400-58691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:58690400-58691200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr11:58690400-58691200	Enhancers	Thymus	Thymus
22	chr11:58690400-58693400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:58690600-58690800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr11:58690600-58690800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:58690600-58690800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:58690600-58690800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:58690600-58690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:58690600-58690800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:58690600-58690800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:58690600-58690800	Flanking Active TSS	HMEC	breast
31	chr11:58690600-58690800	Enhancers	NH-A	brain
32	chr11:58690600-58690800	Enhancers	Osteobl	bone
33	chr11:58690600-58691000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:58690600-58691000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr11:58690600-58691000	Enhancers	Stomach Mucosa	stomach
36	chr11:58690600-58691200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr11:58690600-58691200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr11:58690600-58691200	Enhancers	Primary B cells from peripheral blood	blood
39	chr11:58690600-58691200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr11:58690600-58691200	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:58690600-58691200	Enhancers	Fetal Lung	lung
42	chr11:58690600-58691200	Enhancers	Fetal Thymus	thymus
43	chr11:58690600-58691400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr11:58690600-58691400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:58690600-58691600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr11:58690600-58692000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:58690600-58692000	Enhancers	Liver	Liver
48	chr11:58690600-58692600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr11:58690600-58694000	Weak transcription	Rectal Mucosa Donor 31	rectum

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