Variant report

Variant	rs12272360
Chromosome Location	chr11:73020058-73020059
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	chr11:73018198-73020897	Hela-S3	cervix:	n/a	n/a
2	YY1	chr11:73018772-73020551	A549	lung:	n/a	chr11:73019275-73019284 chr11:73019273-73019287 chr11:73019282-73019291 chr11:73019470-73019484 chr11:73018963-73018975 chr11:73018967-73018975 chr11:73019622-73019633
3	POLR2A	chr11:73020007-73020563	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:73018323-73020776	HCT-116	colon:	n/a	n/a
5	POLR2A	chr11:73018753-73020747	GM12878	blood:	n/a	n/a
6	NFIC	chr11:73017866-73020697	ECC-1	luminal epithelium:	n/a	n/a
7	REST	chr11:73019819-73020409	A549	lung:	n/a	n/a
8	TCF12	chr11:73020052-73020687	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr11:73018316-73020687	Hela-S3	cervix:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225
10	POLR2A	chr11:73020028-73020738	HepG2	liver:	n/a	n/a
11	TEAD4	chr11:73019994-73020749	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr11:73018816-73020726	ECC-1	luminal epithelium:	n/a	n/a
13	SP1	chr11:73019929-73020638	A549	lung:	n/a	chr11:73020374-73020385
14	HCFC1	chr11:73017853-73021101	Hela-S3	cervix:	n/a	n/a
15	MAX	chr11:73018299-73020691	SK-N-SH	brain:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225
16	GABPA	chr11:73019849-73020418	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr11:73019947-73020674	A549	lung:	n/a	n/a
18	POLR2A	chr11:73018776-73020206	GM12892	blood:	n/a	n/a
19	TEAD4	chr11:73019908-73020681	A549	lung:	n/a	n/a
20	MAX	chr11:73018184-73020563	A549	lung:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225
21	HEY1	chr11:73019796-73020789	HepG2	liver:	n/a	n/a
22	EP300	chr11:73019871-73020414	A549	lung:	n/a	n/a
23	SMC3	chr11:73016942-73021131	SK-N-SH	brain:	n/a	chr11:73018484-73018498 chr11:73017587-73017594 chr11:73019010-73019017
24	CEBPB	chr11:73018197-73020491	Hela-S3	cervix:	n/a	n/a
25	SP1	chr11:73019990-73020539	A549	lung:	n/a	chr11:73020374-73020385
26	POLR2A	chr11:73018660-73020754	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr11:73018185-73020781	SK-N-SH	brain:	n/a	chr11:73018579-73018589
28	MAZ	chr11:73018202-73020597	Hela-S3	cervix:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225
29	TEAD4	chr11:73020047-73020632	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:73018720-73020830	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAFK	chr11:73019989-73020124	Hela-S3	cervix:	n/a	n/a
32	ZNF263	chr11:73018906-73020763	HEK293-T-REx	kidney:	n/a	chr11:73019195-73019204
33	POLR2A	chr11:73020049-73020475	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr11:73017906-73020898	ECC-1	luminal epithelium:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225 chr11:73018176-73018186
35	EP300	chr11:73020041-73020580	HepG2	liver:	n/a	n/a
36	RCOR1	chr11:73018273-73020558	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr11:73018797-73020833	MCF10A-Er-Src	breast:	n/a	n/a
38	ZKSCAN1	chr11:73019825-73020445	Hela-S3	cervix:	n/a	n/a
39	SIN3AK20	chr11:73020026-73020684	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr11:73018560-73020828	ProgFib	skin:	n/a	n/a
41	TAF1	chr11:73018028-73020780	ECC-1	luminal epithelium:	n/a	n/a
42	EGR1	chr11:73019108-73020119	ECC-1	luminal epithelium:	n/a	chr11:73019250-73019263 chr11:73019283-73019296 chr11:73019614-73019627 chr11:73019275-73019285 chr11:73019280-73019294 chr11:73019436-73019449 chr11:73019879-73019893 chr11:73019281-73019291 chr11:73019247-73019261 chr11:73019276-73019289 chr11:73019274-73019284 chr11:73019235-73019244
43	POLR2A	chr11:73019981-73020585	H1-hESC	embryonic stem cell:	n/a	n/a
44	CHD1	chr11:73018784-73021132	IMR90	lung:	n/a	n/a
45	TAF1	chr11:73018732-73020680	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr11:73017619-73020165	SK-N-SH	brain:	n/a	chr11:73018482-73018500 chr11:73018485-73018498 chr11:73018483-73018499 chr11:73018765-73018778 chr11:73018484-73018505 chr11:73019470-73019483
47	MAX	chr11:73018203-73020488	GM12878	blood:	n/a	chr11:73019591-73019600 chr11:73019467-73019477 chr11:73019218-73019225
48	CHD1	chr11:73019976-73020481	GM12878	blood:	n/a	n/a
49	MAX	chr11:73019453-73020267	K562	blood:	n/a	chr11:73019591-73019600 chr11:73019467-73019477
50	UBTF	chr11:73019838-73020564	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73003630..73006401-chr11:73018287..73021432,3	MCF-7	breast:
2	chr11:72979299..72983458-chr11:73018365..73020880,3	MCF-7	breast:
3	chr11:72851821..72853715-chr11:73018697..73020407,2	K562	blood:
4	chr11:73019886..73020723-chr11:73087359..73088071,2	Hela-S3	cervix:
5	chr11:73018564..73020076-chr11:73087520..73089366,2	K562	blood:
6	chr11:72980434..72984433-chr11:73015744..73020345,4	MCF-7	breast:
7	chr11:73016708..73020857-chr11:73085853..73088628,6	MCF-7	breast:
8	chr11:72925831..72928740-chr11:73018599..73020225,2	MCF-7	breast:
9	chr11:73015582..73020883-chr11:73085250..73090220,9	MCF-7	breast:
10	chr11:73017077..73020076-chr11:73086849..73089366,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM168A-2	chr11:73019717-73020406	ENSG00000257038.1

Variant related genes	Relation type
ARHGEF17	TF binding region
ENSG00000171631	Chromatin interaction
ENSG00000137478	Chromatin interaction
ENSG00000215841	Chromatin interaction
ENSG00000054967	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1107037	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107038	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107039	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235716	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235718	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11821074	0.83[YRI][hapmap]
rs11826797	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273234	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12279235	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289973	0.95[YRI][hapmap]
rs12290082	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12293779	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310347	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938776	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938779	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017066	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887105	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55664562	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55669228	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732055	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55885773	1.00[ASN][1000 genomes]
rs55921075	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55980420	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012762	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140159	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184513	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56334857	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394842	1.00[ASN][1000 genomes]
rs56665358	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56775065	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59127043	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61749197	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542448	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542460	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941389	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874456	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv520665	chr11:72999221-73061856	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3440775	chr11:73017529-73020077	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3440091	chr11:73018929-73021477	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73017800-73021200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:73018000-73021000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:73018200-73020200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:73018200-73020600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr11:73018200-73020800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr11:73018200-73020800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:73018200-73020800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:73018200-73020800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:73018200-73020800	Active TSS	Ovary	ovary
10	chr11:73018200-73021000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr11:73018200-73021000	Active TSS	Left Ventricle	heart
12	chr11:73018200-73022200	Active TSS	Aorta	Aorta
13	chr11:73018400-73020200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:73018400-73020200	Active TSS	Stomach Smooth Muscle	stomach
15	chr11:73018400-73020400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:73018400-73020400	Active TSS	Fetal Intestine Small	intestine
17	chr11:73018400-73020400	Active TSS	Fetal Muscle Leg	muscle
18	chr11:73018400-73020400	Active TSS	GM12878-XiMat	blood
19	chr11:73018400-73020600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:73018400-73020600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:73018400-73020600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:73018400-73020600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:73018400-73020600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr11:73018400-73020600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:73018400-73020600	Active TSS	Fetal Lung	lung
26	chr11:73018400-73020600	Active TSS	Fetal Stomach	stomach
27	chr11:73018400-73020600	Active TSS	A549	lung
28	chr11:73018400-73020600	Active TSS	Hela-S3	cervix
29	chr11:73018400-73020600	Active TSS	HepG2	liver
30	chr11:73018400-73020600	Active TSS	HUVEC	blood vessel
31	chr11:73018400-73020800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:73018400-73020800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:73018400-73020800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr11:73018400-73020800	Active TSS	Fetal Intestine Large	intestine
35	chr11:73018400-73020800	Active TSS	Right Ventricle	heart
36	chr11:73018400-73020800	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr11:73018400-73020800	Active TSS	Small Intestine	intestine
38	chr11:73018400-73021000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:73018400-73021000	Active TSS	Pancreas	Pancrea
40	chr11:73018400-73021200	Active TSS	HSMM	muscle
41	chr11:73018400-73021200	Active TSS	NHLF	lung
42	chr11:73018400-73021400	Active TSS	Esophagus	oesophagus
43	chr11:73018400-73021400	Active TSS	Fetal Kidney	kidney
44	chr11:73018400-73021600	Active TSS	Brain Angular Gyrus	brain
45	chr11:73018400-73021600	Active TSS	NHDF-Ad	bronchial
46	chr11:73018400-73021800	Active TSS	Brain Cingulate Gyrus	brain
47	chr11:73018400-73021800	Active TSS	Brain Substantia Nigra	brain
48	chr11:73018400-73022000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr11:73018400-73022600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr11:73018400-73022600	Active TSS	Colon Smooth Muscle	Colon

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