Variant report

Variant	rs2452680
Chromosome Location	chr11:65819683-65819684
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	NFIC	chr11:65819458-65820221	GM12878	blood:	n/a	n/a
2	MYC	chr11:65819400-65819874	HepG2	liver:	n/a	chr11:65819555-65819565
3	POLR2A	chr11:65819283-65820058	K562	blood:	n/a	n/a
4	GABPA	chr11:65819322-65820317	HL-60	blood:	n/a	n/a
5	POLR2A	chr11:65819250-65820277	Hela-S3	cervix:	n/a	n/a
6	MAX	chr11:65819276-65820045	H1-hESC	embryonic stem cell:	n/a	chr11:65819555-65819565
7	FOS	chr11:65819641-65819816	MCF10A-Er-Src	breast:	n/a	n/a
8	EBF1	chr11:65819269-65820000	GM12878	blood:	n/a	chr11:65819419-65819432
9	POLR2A	chr11:65819100-65820092	K562	blood:	n/a	n/a
10	GABPA	chr11:65819266-65820375	SK-N-SH	brain:	n/a	n/a
11	RCOR1	chr11:65819510-65819971	GM12878	blood:	n/a	n/a
12	TEAD4	chr11:65819388-65820126	ECC-1	luminal epithelium:	n/a	n/a
13	CREB1	chr11:65819280-65820165	K562	blood:	n/a	n/a
14	ZEB1	chr11:65819288-65820150	GM12878	blood:	n/a	chr11:65819504-65819511
15	TRIM28	chr11:65819346-65819938	K562	blood:	n/a	n/a
16	TBP	chr11:65819324-65819982	Hela-S3	cervix:	n/a	n/a
17	GABPA	chr11:65819419-65820234	HepG2	liver:	n/a	n/a
18	HNF4G	chr11:65819481-65820310	HepG2	liver:	n/a	chr11:65820127-65820139 chr11:65820125-65820140 chr11:65820124-65820142 chr11:65820126-65820139 chr11:65820127-65820139 chr11:65820125-65820140 chr11:65820127-65820139 chr11:65820125-65820140 chr11:65820126-65820140 chr11:65820127-65820139
19	MAX	chr11:65819166-65820211	SK-N-SH	brain:	n/a	chr11:65819555-65819565
20	JUND	chr11:65819415-65819953	HepG2	liver:	n/a	n/a
21	MYC	chr11:65819455-65819948	K562	blood:	n/a	chr11:65819555-65819565
22	YY1	chr11:65819283-65820317	K562	blood:	n/a	chr11:65820107-65820118 chr11:65819568-65819577 chr11:65819401-65819412 chr11:65819851-65819863 chr11:65819845-65819865
23	POLR2A	chr11:65819254-65820090	GM19099	blood:	n/a	n/a
24	POLR2A	chr11:65819146-65820515	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:65819277-65820062	GM12878	blood:	n/a	n/a
26	TAF1	chr11:65819672-65820076	GM12892	blood:	n/a	n/a
27	REST	chr11:65818427-65820727	H1-neurons	neurons:	n/a	chr11:65819271-65819284
28	RELA	chr11:65819079-65820288	GM15510	blood:	n/a	n/a
29	MYC	chr11:65819588-65820260	H1-hESC	embryonic stem cell:	n/a	n/a
30	ELF1	chr11:65819432-65820136	SK-N-SH	brain:	n/a	chr11:65819601-65819613 chr11:65819556-65819568 chr11:65819819-65819830 chr11:65819571-65819580 chr11:65819819-65819830 chr11:65819820-65819829 chr11:65819818-65819831
31	GABPA	chr11:65819244-65820279	K562	blood:	n/a	n/a
32	POLR2A	chr11:65819028-65820088	H1-hESC	embryonic stem cell:	n/a	n/a
33	NRF1	chr11:65819463-65819845	Hela-S3	cervix:	n/a	n/a
34	GTF2B	chr11:65819423-65819925	K562	blood:	n/a	n/a
35	TAF1	chr11:65819333-65820239	HepG2	liver:	n/a	n/a
36	MAX	chr11:65819239-65820166	ECC-1	luminal epithelium:	n/a	chr11:65819555-65819565
37	MAX	chr11:65819289-65820169	MCF-7	breast:	n/a	chr11:65819555-65819565
38	GABPA	chr11:65819318-65820216	HL-60	blood:	n/a	n/a
39	TCF12	chr11:65819154-65820044	GM12878	blood:	n/a	chr11:65819268-65819278
40	NFYB	chr11:65819600-65819898	K562	blood:	n/a	n/a
41	RFX5	chr11:65819314-65820049	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr11:65819170-65820051	K562	blood:	n/a	n/a
43	SMARCB1	chr11:65819312-65820008	Hela-S3	cervix:	n/a	chr11:65819630-65819639
44	MAFK	chr11:65819468-65819886	Hela-S3	cervix:	n/a	n/a
45	MYC	chr11:65819459-65819890	MCF10A-Er-Src	breast:	n/a	chr11:65819555-65819565
46	EP300	chr11:65819568-65819924	GM12878	blood:	n/a	chr11:65819595-65819611 chr11:65819571-65819580 chr11:65819782-65819789 chr11:65819711-65819727
47	POLR2A	chr11:65819169-65820262	MCF-7	breast:	n/a	n/a
48	CREB1	chr11:65819411-65820040	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr11:65819251-65820132	HUVEC	blood vessel:	n/a	n/a
50	ELF1	chr11:65819275-65820355	MCF-7	breast:	n/a	chr11:65819601-65819613 chr11:65819556-65819568 chr11:65819819-65819830 chr11:65819571-65819580 chr11:65819819-65819830 chr11:65819820-65819829 chr11:65819818-65819831 chr11:65819315-65819327

No.	Distal block	Cell Line	Cell type
1	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
2	chr11:65486463..65488167-chr11:65819267..65821152,2	K562	blood:
3	chr11:65778958..65780961-chr11:65818944..65820828,4	MCF-7	breast:
4	chr11:65625573..65627850-chr11:65819625..65821222,2	MCF-7	breast:
5	chr11:65599682..65601863-chr11:65818746..65820444,2	K562	blood:
6	chr11:65769427..65770115-chr11:65819515..65820190,2	K562	blood:
7	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
8	chr11:65767679..65771369-chr11:65818165..65822112,6	MCF-7	breast:
9	chr11:65766270..65769793-chr11:65817988..65822487,7	MCF-7	breast:
10	chr11:65788326..65791572-chr11:65817870..65821514,6	MCF-7	breast:
11	chr11:65624197..65629461-chr11:65817994..65821738,6	K562	blood:
12	chr11:65727969..65730897-chr11:65818847..65821349,3	MCF-7	breast:
13	chr11:65727674..65729529-chr11:65819509..65821064,2	K562	blood:
14	chr11:65666594..65669601-chr11:65818513..65821111,3	K562	blood:
15	chr11:65768250..65771590-chr11:65817294..65821421,6	K562	blood:
16	chr11:65624171..65627161-chr11:65818449..65820914,2	K562	blood:
17	chr11:65686637..65688948-chr11:65818033..65819758,2	MCF-7	breast:
18	chr11:65654406..65656554-chr11:65818022..65819720,2	MCF-7	breast:
19	chr11:65819217..65821138-chr15:96872080..96874468,2	MCF-7	breast:
20	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
21	chr11:65429132..65431872-chr11:65817636..65822281,4	MCF-7	breast:
22	chr11:65768250..65771110-chr11:65819143..65821313,2	K562	blood:
23	chr11:65818576..65820605-chr11:66044652..66046444,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SF3B2-1	chr11:65819364-65819790	NONHSAT022260
2	lnc-GAL3ST3-1	chr11:65818545-65820124	ncRnaDb_ncrna_FR023308_1

Variant related genes	Relation type
GAL3ST3	TF binding region
SF3B2	TF binding region
ENSG00000238752	TF binding region
ENSG00000175376	Chromatin interaction
ENSG00000172803	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000254452	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000185551	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000245156	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000174871	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1049872	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203998	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs12416952	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12416953	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12421022	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12803276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17147325	0.81[JPT][hapmap]
rs17147371	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs1893316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2000672	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33988687	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34073119	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34114713	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35611816	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741370	1.00[GIH][hapmap]
rs477280	0.82[EUR][1000 genomes]
rs491618	0.80[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4930333	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930337	0.84[JPT][hapmap]
rs4930340	0.84[JPT][hapmap]
rs503156	0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs535752	0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs547404	0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs557799	0.84[EUR][1000 genomes]
rs570887	0.82[EUR][1000 genomes]
rs574153	0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs61895579	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873491	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs947847	0.92[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2452680	SYT12	cis	parietal	SCAN
rs2452680	RBM14	cis	cerebellum	SCAN
rs2452680	TBC1D10C	cis	cerebellum	SCAN
rs2452680	SF3B2	cis	parietal	SCAN
rs2452680	SLC22A6	cis	cerebellum	SCAN
rs2452680	SF3B2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65818200-65819800	Enhancers	Stomach Mucosa	stomach
2	chr11:65818800-65820200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:65818800-65820400	Active TSS	Rectal Smooth Muscle	rectum
4	chr11:65818800-65820600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr11:65818800-65820800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr11:65818800-65821000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr11:65818800-65821000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr11:65819000-65819800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:65819000-65820400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:65819000-65820400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:65819000-65820400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:65819000-65820400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr11:65819000-65820400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:65819000-65820400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:65819000-65820400	Active TSS	Brain Substantia Nigra	brain
16	chr11:65819000-65820400	Active TSS	Fetal Brain Female	brain
17	chr11:65819000-65820400	Active TSS	Ovary	ovary
18	chr11:65819000-65820400	Active TSS	Placenta Amnion	Placenta Amnion
19	chr11:65819000-65820400	Active TSS	K562	blood
20	chr11:65819000-65820600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:65819000-65820600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr11:65819000-65820600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:65819000-65820600	Active TSS	Gastric	stomach
24	chr11:65819000-65820600	Active TSS	Left Ventricle	heart
25	chr11:65819000-65820600	Active TSS	Psoas Muscle	Psoas
26	chr11:65819000-65820800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:65819000-65820800	Active TSS	Aorta	Aorta
28	chr11:65819000-65820800	Active TSS	Right Atrium	heart
29	chr11:65819000-65821000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr11:65819200-65819800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:65819200-65820000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr11:65819200-65820000	Active TSS	Brain Germinal Matrix	brain
33	chr11:65819200-65820000	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr11:65819200-65820000	Active TSS	Dnd41	blood
35	chr11:65819200-65820000	Active TSS	HepG2	liver
36	chr11:65819200-65820200	Active TSS	Primary T cells from cord blood	blood
37	chr11:65819200-65820200	Active TSS	Brain Angular Gyrus	brain
38	chr11:65819200-65820200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr11:65819200-65820400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:65819200-65820400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:65819200-65820400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr11:65819200-65820400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:65819200-65820400	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr11:65819200-65820400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:65819200-65820400	Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr11:65819200-65820400	Active TSS	Brain Anterior Caudate	brain
47	chr11:65819200-65820400	Active TSS	Brain Cingulate Gyrus	brain
48	chr11:65819200-65820400	Active TSS	Colon Smooth Muscle	Colon
49	chr11:65819200-65820400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr11:65819200-65820400	Active TSS	Fetal Brain Male	brain

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