Variant report

Variant	rs2450104
Chromosome Location	chr12:56655658-56655659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:56655488-56656122	A549	lung:	n/a	n/a
2	MYC	chr12:56655599-56656003	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr12:56655381-56656184	SK-N-SH	brain:	n/a	n/a
4	FOS	chr12:56655601-56655983	MCF10A-Er-Src	breast:	n/a	n/a
5	USF1	chr12:56655548-56656173	HCT-116	colon:	n/a	n/a
6	EP300	chr12:56655258-56656093	A549	lung:	n/a	n/a
7	USF1	chr12:56655616-56656142	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr12:56655416-56656092	SK-N-SH	brain:	n/a	n/a
9	JUND	chr12:56655466-56655999	Hela-S3	cervix:	n/a	chr12:56655514-56655523
10	MAX	chr12:56655380-56656161	A549	lung:	n/a	n/a
11	RCOR1	chr12:56655376-56655998	Hela-S3	cervix:	n/a	n/a
12	USF1	chr12:56655570-56656179	A549	lung:	n/a	n/a
13	FOS	chr12:56655600-56656003	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF12	chr12:56655259-56656129	A549	lung:	n/a	n/a
15	PBX3	chr12:56655575-56656062	SK-N-SH	brain:	n/a	n/a
16	FOSL2	chr12:56655462-56656084	SK-N-SH	brain:	n/a	chr12:56655514-56655523
17	SP1	chr12:56655362-56656182	A549	lung:	n/a	n/a
18	MAX	chr12:56655605-56655991	Hela-S3	cervix:	n/a	n/a
19	FOSL2	chr12:56655523-56656074	SK-N-SH	brain:	n/a	n/a
20	TBP	chr12:56655562-56655943	Hela-S3	cervix:	n/a	n/a
21	SMC3	chr12:56655656-56656055	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:56655589-56656004	SK-N-SH	brain:	n/a	n/a
23	FOS	chr12:56655651-56655958	MCF10A-Er-Src	breast:	n/a	n/a
24	USF1	chr12:56655640-56656093	ECC-1	luminal epithelium:	n/a	n/a
25	SP1	chr12:56655285-56656187	A549	lung:	n/a	n/a
26	USF1	chr12:56655597-56656098	A549	lung:	n/a	n/a
27	POLR2A	chr12:56655308-56655968	U87	brain:	n/a	n/a
28	TEAD4	chr12:56655549-56656021	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr12:56655548-56655905	Hela-S3	cervix:	n/a	n/a
30	FOSL2	chr12:56655325-56656111	A549	lung:	n/a	chr12:56655514-56655523
31	MAX	chr12:56655154-56656175	A549	lung:	n/a	n/a
32	FOXA2	chr12:56655575-56656036	A549	lung:	n/a	n/a
33	FOSL1	chr12:56655486-56656163	HCT-116	colon:	n/a	chr12:56655514-56655523
34	USF1	chr12:56655589-56656000	A549	lung:	n/a	n/a
35	JUND	chr12:56655547-56655958	A549	lung:	n/a	n/a
36	FOSL2	chr12:56655555-56655980	A549	lung:	n/a	n/a
37	USF1	chr12:56655472-56656084	A549	lung:	n/a	n/a
38	USF1	chr12:56655568-56656130	A549	lung:	n/a	n/a
39	RCOR1	chr12:56655417-56655973	K562	blood:	n/a	n/a
40	RFX5	chr12:56655502-56655978	Hela-S3	cervix:	n/a	n/a
41	FOS	chr12:56655604-56655983	MCF10A-Er-Src	breast:	n/a	n/a
42	TEAD4	chr12:56655444-56656193	A549	lung:	n/a	n/a
43	USF1	chr12:56655613-56656066	A549	lung:	n/a	n/a
44	JUN	chr12:56655494-56655982	Hela-S3	cervix:	n/a	chr12:56655514-56655523

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56655285..56657281-chr12:56708126..56709828,2	MCF-7	breast:
2	chr12:56654088..56655986-chr12:56677817..56679914,2	K562	blood:
3	chr12:56650896..56653436-chr12:56654536..56656927,2	K562	blood:
4	chr12:56586858..56587653-chr12:56655157..56655879,2	K562	blood:
5	chr12:56649740..56653860-chr12:56655193..56656927,5	K562	blood:
6	chr12:56654817..56657180-chr12:56660421..56662698,2	K562	blood:
7	chr12:56613899..56621490-chr12:56648204..56656770,13	K562	blood:
8	chr12:56581956..56584923-chr12:56653937..56655970,4	MCF-7	breast:
9	chr12:56652145..56655661-chr12:56692434..56696303,4	MCF-7	breast:
10	chr12:56617361..56619485-chr12:56654340..56655960,2	K562	blood:
11	chr12:56585119..56588014-chr12:56654037..56656404,3	MCF-7	breast:
12	chr12:56650621..56658058-chr12:56658155..56662259,11	MCF-7	breast:

No data

Variant related genes	Relation type
ANKRD52	TF binding region
COQ10A	TF binding region
ENSG00000257303	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139613	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10747762	0.91[AMR][1000 genomes]
rs11171774	1.00[AMR][1000 genomes]
rs11575218	1.00[MEX][hapmap];0.82[MKK][hapmap]
rs1274492	0.82[AFR][1000 genomes]
rs1274501	1.00[AMR][1000 genomes]
rs17118576	1.00[MEX][hapmap]
rs1995742	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2066811	0.81[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs2450101	0.91[AMR][1000 genomes]
rs2629449	0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35382885	1.00[MEX][hapmap]
rs4759219	1.00[AMR][1000 genomes]
rs7301099	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs773644	0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs773647	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56652800-56660200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56652800-56660200	Weak transcription	Esophagus	oesophagus
3	chr12:56652800-56660200	Weak transcription	Left Ventricle	heart
4	chr12:56653000-56659400	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:56653000-56659600	Weak transcription	Right Ventricle	heart
6	chr12:56653000-56659800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:56653000-56659800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:56653000-56659800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:56653000-56660000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:56653000-56660000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:56653000-56660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:56653000-56660000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:56653000-56660000	Weak transcription	Brain Anterior Caudate	brain
14	chr12:56653000-56660000	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:56653000-56660000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:56653000-56660000	Weak transcription	HUVEC	blood vessel
17	chr12:56653000-56660200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:56653000-56660200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:56653000-56660400	Weak transcription	Gastric	stomach
20	chr12:56653200-56660000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:56653200-56660000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:56653200-56660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:56653200-56660000	Weak transcription	Brain Germinal Matrix	brain
24	chr12:56653200-56660000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:56653400-56660200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:56654200-56656200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:56654200-56656200	Enhancers	Hela-S3	cervix
28	chr12:56654200-56656600	Enhancers	HSMMtube	muscle
29	chr12:56654400-56656000	Enhancers	Fetal Muscle Leg	muscle
30	chr12:56654600-56656000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:56654600-56656200	Enhancers	HSMM	muscle
32	chr12:56654800-56655800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:56654800-56656000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:56654800-56656000	Enhancers	K562	blood
35	chr12:56654800-56656200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:56654800-56656200	Enhancers	Fetal Intestine Large	intestine
37	chr12:56654800-56656200	Enhancers	HMEC	breast
38	chr12:56655000-56656000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:56655000-56656000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:56655000-56656000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr12:56655000-56656000	Enhancers	Placenta	Placenta
42	chr12:56655200-56656000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:56655200-56656000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:56655200-56656200	Enhancers	Fetal Intestine Small	intestine
45	chr12:56655200-56656200	Enhancers	NHLF	lung
46	chr12:56655200-56656200	Enhancers	Osteobl	bone
47	chr12:56655400-56655800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:56655400-56656000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:56655400-56656000	Flanking Active TSS	A549	lung
50	chr12:56655400-56656000	Enhancers	HepG2	liver

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