Variant report

Variant	rs61110645
Chromosome Location	chr12:123570455-123570456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:81)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:81 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:123570279-123570695	Hela-S3	cervix:	n/a	n/a
2	SMARCC1	chr12:123570275-123571339	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr12:123570340-123570490	HMEC	breast:	n/a	n/a
4	CTCF	chr12:123570360-123570510	HBMEC	blood vessel:	n/a	n/a
5	FOSL1	chr12:123570003-123570935	HCT-116	colon:	n/a	n/a
6	BCL3	chr12:123570170-123570834	A549	lung:	n/a	n/a
7	SP1	chr12:123570159-123570825	A549	lung:	n/a	n/a
8	MXI1	chr12:123570373-123570545	HepG2	liver:	n/a	n/a
9	MAX	chr12:123570402-123570602	A549	lung:	n/a	n/a
10	FOS	chr12:123570316-123570656	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
11	TFAP2C	chr12:123570294-123570897	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr12:123570277-123570590	SK-N-SH_RA	brain:	n/a	n/a
13	NFIC	chr12:123570183-123570795	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr12:123570320-123570470	BE2_C	brain:	n/a	n/a
15	EP300	chr12:123570370-123570689	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr12:123570399-123570905	MCF10A-Er-Src	breast:	n/a	chr12:123570533-123570544
17	NFYB	chr12:123570374-123570568	GM12878	blood:	n/a	n/a
18	CTCF	chr12:123570320-123570470	NHEK	skin:	n/a	n/a
19	BHLHE40	chr12:123570409-123570469	A549	lung:	n/a	n/a
20	CTCF	chr12:123570360-123570510	HRPEpiC	eye:	n/a	n/a
21	FOSL2	chr12:123570263-123570775	SK-N-SH	brain:	n/a	n/a
22	MYC	chr12:123570421-123570460	HUVEC	blood vessel:	n/a	n/a
23	EP300	chr12:123570190-123570754	A549	lung:	n/a	n/a
24	CTCF	chr12:123570340-123570490	HCT-116	colon:	n/a	n/a
25	MYC	chr12:123570339-123570635	MCF10A-Er-Src	breast:	n/a	n/a
26	NFIC	chr12:123570232-123570790	SK-N-SH	brain:	n/a	n/a
27	CEBPB	chr12:123570377-123570708	Hela-S3	cervix:	n/a	n/a
28	MAFK	chr12:123570415-123570615	Hela-S3	cervix:	n/a	n/a
29	JUND	chr12:123570235-123570727	A549	lung:	n/a	n/a
30	RAD21	chr12:123570322-123570600	A549	lung:	n/a	n/a
31	SP1	chr12:123570054-123570950	HCT-116	colon:	n/a	n/a
32	RFX5	chr12:123570333-123570721	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:123570241-123570713	HCT-116	colon:	n/a	n/a
34	POLR2A	chr12:123570301-123570656	HCT-116	colon:	n/a	n/a
35	CHD2	chr12:123570389-123570639	Hela-S3	cervix:	n/a	n/a
36	TCF12	chr12:123570113-123570884	SK-N-SH	brain:	n/a	n/a
37	FOS	chr12:123570236-123570664	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
38	CTCF	chr12:123570380-123570530	GM12872	blood:	n/a	n/a
39	CTCF	chr12:123570320-123570470	RPTEC	kidney:	n/a	n/a
40	FOS	chr12:123570311-123570622	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
41	STAT1	chr12:123570275-123570828	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr12:123570378-123570757	Hela-S3	cervix:	n/a	n/a
43	STAT3	chr12:123570337-123570779	MCF10A-Er-Src	breast:	n/a	chr12:123570533-123570544
44	POLR2A	chr12:123570343-123570584	U87	brain:	n/a	n/a
45	TCF12	chr12:123570143-123570905	A549	lung:	n/a	n/a
46	NR3C1	chr12:123570250-123570722	A549	lung:	n/a	n/a
47	CTCF	chr12:123570400-123570550	GM12872	blood:	n/a	n/a
48	POLR2A	chr12:123570449-123570646	Hela-S3	cervix:	n/a	n/a
49	EP300	chr12:123570280-123570680	SK-N-SH_RA	brain:	n/a	n/a
50	NR3C1	chr12:123570288-123570691	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123570325..123572939-chr12:123584835..123587723,2	K562	blood:
2	chr12:123463347..123466075-chr12:123569459..123571842,3	MCF-7	breast:
3	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
4	chr12:123558670..123560288-chr12:123570276..123571928,2	MCF-7	breast:
5	chr12:123564490..123568285-chr12:123569418..123571923,3	MCF-7	breast:
6	chr12:123553938..123556177-chr12:123569244..123571363,2	MCF-7	breast:
7	chr12:123558779..123562598-chr12:123568640..123572609,6	MCF-7	breast:

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000182196	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000251497	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs4427600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55820451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56846082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.80[AFR][1000 genomes]
rs58282663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490757	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59995499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60167440	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60235187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60320128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60894374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61089898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61396549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.80[AFR][1000 genomes]
rs73413223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413226	0.80[AFR][1000 genomes]
rs73413228	0.80[AFR][1000 genomes]
rs73413230	0.80[AFR][1000 genomes]
rs73413241	0.80[AFR][1000 genomes]
rs73413246	0.80[AFR][1000 genomes]
rs7964036	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123560600-123574200	Weak transcription	Gastric	stomach
2	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
3	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
5	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:123562200-123572600	Weak transcription	K562	blood
7	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
9	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
10	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:123566400-123571600	Enhancers	Right Atrium	heart
12	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:123566600-123571600	Enhancers	Lung	lung
14	chr12:123567200-123570800	Enhancers	Liver	Liver
15	chr12:123567200-123570800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
17	chr12:123567800-123571600	Enhancers	Fetal Muscle Leg	muscle
18	chr12:123568000-123570600	Enhancers	Psoas Muscle	Psoas
19	chr12:123568000-123570800	Enhancers	Fetal Muscle Trunk	muscle
20	chr12:123568000-123571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:123568000-123571400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:123568000-123571400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:123568200-123570800	Enhancers	Stomach Smooth Muscle	stomach
24	chr12:123568200-123571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:123568200-123571400	Enhancers	Brain Anterior Caudate	brain
26	chr12:123568400-123570600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:123568400-123570600	Enhancers	HSMMtube	muscle
28	chr12:123568400-123571000	Enhancers	Primary hematopoietic stem cells	blood
29	chr12:123568400-123571400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:123568400-123571600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:123568600-123570600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:123568600-123571000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
34	chr12:123568800-123571600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:123568800-123571800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:123569000-123570600	Enhancers	GM12878-XiMat	blood
38	chr12:123569000-123570800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:123569000-123574000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:123569200-123570600	Weak transcription	Adipose Nuclei	Adipose
41	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr12:123569400-123570600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr12:123569400-123571000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr12:123569400-123571000	Enhancers	Spleen	Spleen
46	chr12:123569400-123574600	Enhancers	Primary B cells from peripheral blood	blood
47	chr12:123569600-123570600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:123569600-123570600	Enhancers	Brain Hippocampus Middle	brain
49	chr12:123569600-123570800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:123569600-123570800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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