Variant report

Variant	rs11820828
Chromosome Location	chr11:58672716-58672717
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	chr11:58672608-58673190	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:58672599-58673171	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr11:58672657-58673600	H1-neurons	neurons:	n/a	n/a
4	PBX3	chr11:58672570-58673851	SK-N-SH	brain:	n/a	chr11:58673417-58673437
5	TAF1	chr11:58672539-58673636	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr11:58672599-58673118	H1-hESC	embryonic stem cell:	n/a	chr11:58672877-58672891
7	ZNF263	chr11:58671256-58673866	HEK293-T-REx	kidney:	n/a	chr11:58671955-58671976 chr11:58671880-58671889
8	RCOR1	chr11:58672269-58673181	IMR90	lung:	n/a	n/a
9	TBP	chr11:58672670-58673742	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr11:58672506-58673760	SK-N-SH	brain:	n/a	chr11:58673548-58673559
11	E2F6	chr11:58672587-58673855	H1-hESC	embryonic stem cell:	n/a	chr11:58673476-58673483 chr11:58673476-58673483 chr11:58673272-58673281 chr11:58673472-58673484 chr11:58673476-58673483 chr11:58673475-58673484
12	POLR2A	chr11:58672606-58673707	H1-neurons	neurons:	n/a	n/a
13	CHD1	chr11:58672403-58673216	IMR90	lung:	n/a	n/a
14	MAX	chr11:58672483-58673931	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
15	KAP1	chr11:58672432-58673114	HEK293	kidney:	n/a	n/a
16	E2F6	chr11:58672534-58674084	H1-hESC	embryonic stem cell:	n/a	chr11:58673476-58673483 chr11:58673476-58673483 chr11:58673272-58673281 chr11:58673472-58673484 chr11:58673476-58673483 chr11:58673475-58673484
17	POLR2A	chr11:58672600-58673435	IMR90	lung:	n/a	n/a
18	PBX3	chr11:58672601-58673789	SK-N-SH	brain:	n/a	chr11:58673417-58673437
19	POLR2A	chr11:58672554-58673695	H1-neurons	neurons:	n/a	n/a
20	SIN3A	chr11:58672415-58673795	H1-hESC	embryonic stem cell:	n/a	chr11:58673223-58673234
21	MXI1	chr11:58672155-58674226	SK-N-SH	brain:	n/a	n/a
22	YY1	chr11:58672714-58673155	SK-N-SH_RA	brain:	n/a	chr11:58672877-58672891
23	MXI1	chr11:58672556-58672962	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr11:58672477-58673886	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
25	POLR2A	chr11:58672544-58673353	ProgFib	skin:	n/a	n/a
26	POLR2A	chr11:58672473-58673794	H1-hESC	embryonic stem cell:	n/a	n/a
27	KAP1	chr11:58672489-58672992	U2OS	brain:	n/a	n/a
28	TAF1	chr11:58672460-58673168	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr11:58672664-58673746	H1-hESC	embryonic stem cell:	n/a	n/a
30	REST	chr11:58672357-58673922	H1-neurons	neurons:	n/a	chr11:58672832-58672852 chr11:58672763-58672776 chr11:58672833-58672851 chr11:58672832-58672852
31	POLR2A	chr11:58672594-58673531	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr11:58672700-58672850	HEEpiC	esophagus:	n/a	n/a
33	CHD2	chr11:58672662-58673757	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3AK20	chr11:58672633-58672977	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr11:58672546-58673203	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr11:58672611-58672929	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58672702-58672752	NH-A	brain:	n/a
2	chr11:58672702-58672752	HCPEpiC	choroid plexus:	n/a
3	chr11:58672702-58672752	SK-N-SH	brain:	n/a
4	chr11:58672702-58672752	AG10803	skin:	n/a
5	chr11:58672702-58672752	HCT-116	colon:	n/a
6	chr11:58672702-58672752	NB4	blood:	n/a
7	chr11:58672702-58672752	HAEpiC	amniotic membrane:	n/a
8	chr11:58672702-58672752	Hepatocyte	liver:	n/a
9	chr11:58672702-58672752	PANC-1	pancreas:	n/a
10	chr11:58672702-58672752	GM12891	blood:	n/a
11	chr11:58672702-58672752	GM06990	blood:	n/a
12	chr11:58672702-58672752	HepG2	liver:	n/a
13	chr11:58672702-58672752	HUVEC	blood vessel:	n/a
14	chr11:58672702-58672752	MCF10A-Er-Src	breast:	n/a
15	chr11:58672702-58672752	GM12878	blood:	n/a
16	chr11:58672702-58672752	AG09309	skin:	n/a
17	chr11:58672702-58672752	HPAEpiC	pulmonary alveolar:	n/a
18	chr11:58672702-58672752	PFSK-1	brain:	n/a
19	chr11:58672702-58672752	HRPEpiC	eye:	n/a
20	chr11:58672702-58672752	HRCEpiC	kidney:	n/a
21	chr11:58672702-58672752	NT2-D1	testis:	n/a
22	chr11:58672702-58672752	AG04449	skin:	fetal
23	chr11:58672702-58672752	SAEC	small airway:	n/a
24	chr11:58672702-58672752	NHDF-neo	bronchial:	n/a
25	chr11:58672702-58672752	HMEC	breast:	n/a
26	chr11:58672702-58672752	Jurkat	blood:	n/a
27	chr11:58672702-58672752	GM19239	blood:	n/a
28	chr11:58672702-58672752	AoSMC	blood vessel:	n/a
29	chr11:58672702-58672752	ECC-1	luminal epithelium:	n/a
30	chr11:58672702-58672752	HCF	heart:	n/a
31	chr11:58672702-58672752	GM12892	blood:	n/a
32	chr11:58672702-58672752	CMK	blood:	n/a
33	chr11:58672702-58672752	BE2_C	brain:	n/a
34	chr11:58672702-58672752	LNCaP	prostate:	n/a
35	chr11:58672702-58672752	Caco-2	colon:	n/a
36	chr11:58672702-58672752	K562	blood:	n/a
37	chr11:58672702-58672752	SK-N-MC	brain:	n/a
38	chr11:58672702-58672752	BJ	skin:	n/a
39	chr11:58672702-58672752	U87	brain:	n/a
40	chr11:58672702-58672752	HRE	kidney:	n/a
41	chr11:58672702-58672752	SK-N-SH_RA	brain:	n/a
42	chr11:58672702-58672752	HNPCEpiC	eye:	n/a
43	chr11:58672702-58672752	HIPEpiC	eye:	n/a
44	chr11:58672702-58672752	PrEC	prostate:	n/a
45	chr11:58672702-58672752	SKMC	muscle:	n/a
46	chr11:58672702-58672752	Hela-S3	cervix:	n/a
47	chr11:58672702-58672752	HCM	heart:	n/a
48	chr11:58672702-58672752	ProgFib	skin:	n/a
49	chr11:58672702-58672752	H1-hESC	embryonic stem cell:	embryo
50	chr11:58672702-58672752	RPTEC	kidney:	n/a

Variant related genes	Relation type
GLYATL1	TF binding region
ENSG00000224130	TF binding region
GLYATL2	TF binding region
GLYATL1	CpG island
ENSG00000224130	CpG island
GLYATL2	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1806567	1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59155521	1.00[EUR][1000 genomes]
rs73481069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73481080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1045858	chr11:58547772-58674568	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1052173	chr11:58553516-58678496	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58671200-58673400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:58671200-58673800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:58671200-58673800	Active TSS	NHLF	lung
4	chr11:58671400-58673000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr11:58671400-58673600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:58671400-58673800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:58671400-58673800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr11:58671600-58673200	Flanking Active TSS	HMEC	breast
9	chr11:58671800-58672800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:58671800-58672800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr11:58671800-58673400	Active TSS	NH-A	brain
12	chr11:58672000-58673600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr11:58672000-58673600	Active TSS	Fetal Brain Female	brain
14	chr11:58672000-58673600	Active TSS	NHDF-Ad	bronchial
15	chr11:58672200-58673200	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr11:58672200-58673400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
17	chr11:58672200-58673600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:58672200-58673600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:58672200-58673600	Active TSS	Fetal Brain Male	brain
20	chr11:58672200-58674000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr11:58672400-58672800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr11:58672400-58672800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:58672400-58672800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr11:58672400-58672800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:58672400-58672800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:58672400-58672800	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr11:58672400-58672800	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr11:58672400-58672800	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr11:58672400-58672800	Bivalent/Poised TSS	Fetal Lung	lung
30	chr11:58672400-58673000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:58672400-58673000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:58672400-58673000	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr11:58672400-58673000	Flanking Active TSS	NHEK	skin
34	chr11:58672400-58673200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:58672400-58673200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:58672400-58673200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:58672400-58673200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:58672400-58673200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr11:58672400-58673400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
40	chr11:58672400-58673400	Active TSS	Brain Germinal Matrix	brain
41	chr11:58672400-58673600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr11:58672400-58673600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:58672400-58673600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:58672400-58673600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr11:58672400-58673600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:58672400-58673600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:58672400-58673600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
48	chr11:58672400-58673600	Active TSS	A549	lung
49	chr11:58672400-58673800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:58672400-58673800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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