Variant report

Variant	rs6591500
Chromosome Location	chr11:58673538-58673539
allele	A/C
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	CTCF	chr11:58673460-58673610	HRE	kidney:	n/a	n/a
2	KAP1	chr11:58673346-58674014	U2OS	brain:	n/a	n/a
3	CTCF	chr11:58673520-58673670	NHEK	skin:	n/a	n/a
4	SP1	chr11:58673224-58673667	A549	lung:	n/a	chr11:58673375-58673396
5	MYC	chr11:58673292-58673580	MCF10A-Er-Src	breast:	n/a	chr11:58673548-58673559
6	TAF1	chr11:58672657-58673600	H1-neurons	neurons:	n/a	n/a
7	PBX3	chr11:58672570-58673851	SK-N-SH	brain:	n/a	chr11:58673417-58673437
8	MAX	chr11:58673236-58673796	SK-N-SH	brain:	n/a	chr11:58673548-58673559
9	TAF1	chr11:58672539-58673636	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr11:58673440-58673808	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr11:58673440-58673710	BE2_C	brain:	n/a	n/a
12	SP1	chr11:58673084-58673766	H1-hESC	embryonic stem cell:	n/a	chr11:58673696-58673708 chr11:58673168-58673177 chr11:58673697-58673706 chr11:58673696-58673708 chr11:58673375-58673396
13	GTF2F1	chr11:58672793-58673732	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:58673150-58673674	SK-N-MC	brain:	n/a	n/a
15	ZNF263	chr11:58671256-58673866	HEK293-T-REx	kidney:	n/a	chr11:58671955-58671976 chr11:58671880-58671889
16	MAX	chr11:58673205-58673848	A549	lung:	n/a	chr11:58673548-58673559
17	MAX	chr11:58673298-58673834	A549	lung:	n/a	chr11:58673548-58673559
18	RAD21	chr11:58673423-58673751	H1-hESC	embryonic stem cell:	n/a	n/a
19	TBP	chr11:58672670-58673742	H1-hESC	embryonic stem cell:	n/a	n/a
20	SETDB1	chr11:58673333-58673664	U2OS	brain:	n/a	n/a
21	USF1	chr11:58673363-58673647	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr11:58673460-58673610	GM12865	blood:	n/a	n/a
23	CTCF	chr11:58673520-58673670	BJ	skin:	n/a	n/a
24	SP2	chr11:58673182-58673618	H1-hESC	embryonic stem cell:	n/a	chr11:58673416-58673439 chr11:58673412-58673422
25	MAX	chr11:58672506-58673760	SK-N-SH	brain:	n/a	chr11:58673548-58673559
26	TCF12	chr11:58673350-58673680	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr11:58673294-58673677	H1-hESC	embryonic stem cell:	n/a	n/a
28	HDAC2	chr11:58673408-58673695	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F6	chr11:58673223-58673788	A549	lung:	n/a	chr11:58673476-58673483 chr11:58673476-58673483 chr11:58673272-58673281 chr11:58673472-58673484 chr11:58673476-58673483 chr11:58673475-58673484
30	CTCF	chr11:58673500-58673650	AG10803	skin:	n/a	n/a
31	E2F4	chr11:58673264-58673835	MCF10A-Er-Src	breast:	n/a	chr11:58673476-58673483 chr11:58673476-58673483 chr11:58673272-58673281 chr11:58673472-58673484 chr11:58673476-58673483 chr11:58673475-58673484
32	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
33	MYC	chr11:58673267-58673582	MCF10A-Er-Src	breast:	n/a	chr11:58673548-58673559
34	POLR2A	chr11:58672606-58673707	H1-neurons	neurons:	n/a	n/a
35	ZNF143	chr11:58673325-58673864	H1-hESC	embryonic stem cell:	n/a	chr11:58673434-58673453
36	CTCF	chr11:58673526-58673851	K562	blood:	n/a	n/a
37	MAX	chr11:58672483-58673931	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
38	CTCF	chr11:58673414-58673824	IMR90	lung:	n/a	n/a
39	BHLHE40	chr11:58673515-58673655	K562	blood:	n/a	n/a
40	CTCF	chr11:58673520-58673670	SK-N-SH_RA	brain:	n/a	n/a
41	NFYB	chr11:58672958-58673606	K562	blood:	n/a	chr11:58673376-58673386 chr11:58673411-58673425 chr11:58673374-58673388
42	REST	chr11:58673388-58673644	SK-N-SH	brain:	n/a	n/a
43	CTCF	chr11:58673519-58673778	K562	blood:	n/a	n/a
44	REST	chr11:58673405-58673646	SK-N-SH	brain:	n/a	n/a
45	NFYA	chr11:58673296-58673557	K562	blood:	n/a	chr11:58673376-58673386 chr11:58673411-58673425 chr11:58673374-58673388
46	FOS	chr11:58673282-58673540	MCF10A-Er-Src	breast:	n/a	n/a
47	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
48	CTCF	chr11:58673500-58673650	HPAF	blood vessel:	n/a	n/a
49	MYC	chr11:58673354-58673782	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
50	PBX3	chr11:58672601-58673789	SK-N-SH	brain:	n/a	chr11:58673417-58673437

Variant related genes	Relation type
GLYATL2	TF binding region

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

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

rs_ID	r²[population]
rs1788524	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1788538	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1788550	0.93[ASN][1000 genomes]
rs472554	0.95[ASN][1000 genomes]
rs474253	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs481247	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs486950	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs487309	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs487920	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs488737	0.92[ASN][1000 genomes]
rs489732	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs494149	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs500462	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs503591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503918	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]
rs513877	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs517039	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs517387	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs522376	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs530180	0.95[ASN][1000 genomes]
rs531578	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534890	0.95[ASN][1000 genomes]
rs538678	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs541258	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs544800	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs552591	0.81[CEU][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs565355	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs573322	0.80[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs577190	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs578396	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs578610	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7945540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58671200-58673800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:58671200-58673800	Active TSS	NHLF	lung
3	chr11:58671400-58673600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:58671400-58673800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:58671400-58673800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr11:58672000-58673600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr11:58672000-58673600	Active TSS	Fetal Brain Female	brain
8	chr11:58672000-58673600	Active TSS	NHDF-Ad	bronchial
9	chr11:58672200-58673600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:58672200-58673600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:58672200-58673600	Active TSS	Fetal Brain Male	brain
12	chr11:58672200-58674000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr11:58672400-58673600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr11:58672400-58673600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:58672400-58673600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:58672400-58673600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr11:58672400-58673600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:58672400-58673600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:58672400-58673600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
20	chr11:58672400-58673600	Active TSS	A549	lung
21	chr11:58672400-58673800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:58672400-58673800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:58672400-58673800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:58672400-58673800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:58672400-58673800	Active TSS	Fetal Kidney	kidney
26	chr11:58672400-58673800	Active TSS	HSMM	muscle
27	chr11:58672400-58673800	Active TSS	Osteobl	bone
28	chr11:58672600-58673600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr11:58672600-58673600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr11:58672600-58673600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:58672600-58673600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:58672600-58673600	Bivalent/Poised TSS	Colonic Mucosa	Colon
33	chr11:58672600-58673600	Enhancers	Lung	lung
34	chr11:58672600-58673600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
35	chr11:58672600-58673600	Bivalent/Poised TSS	HUVEC	blood vessel
36	chr11:58672600-58673800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr11:58672600-58673800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr11:58672600-58673800	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr11:58672600-58673800	Active TSS	Brain Substantia Nigra	brain
40	chr11:58672600-58673800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr11:58672600-58673800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr11:58672600-58674000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr11:58672600-58674000	Bivalent Enhancer	Placenta	Placenta
44	chr11:58672800-58673600	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr11:58672800-58673600	Active TSS	Fetal Lung	lung
46	chr11:58672800-58673800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:58672800-58673800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:58672800-58673800	Active TSS	Brain Hippocampus Middle	brain
49	chr11:58672800-58673800	Active TSS	HSMMtube	muscle
50	chr11:58672800-58674000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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