Variant report

Variant	rs60320128
Chromosome Location	chr12:123570348-123570349
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 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	FOSL1	chr12:123570003-123570935	HCT-116	colon:	n/a	n/a
5	BCL3	chr12:123570170-123570834	A549	lung:	n/a	n/a
6	SP1	chr12:123570159-123570825	A549	lung:	n/a	n/a
7	CTCF	chr12:123570300-123570450	HEEpiC	esophagus:	n/a	n/a
8	FOS	chr12:123570316-123570656	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
9	TFAP2C	chr12:123570294-123570897	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr12:123570277-123570590	SK-N-SH_RA	brain:	n/a	n/a
11	NFIC	chr12:123570183-123570795	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr12:123570320-123570470	BE2_C	brain:	n/a	n/a
13	CTCF	chr12:123570280-123570430	MCF-7	breast:	n/a	n/a
14	CTCF	chr12:123570320-123570470	NHEK	skin:	n/a	n/a
15	FOSL2	chr12:123570263-123570775	SK-N-SH	brain:	n/a	n/a
16	EP300	chr12:123570190-123570754	A549	lung:	n/a	n/a
17	CTCF	chr12:123570240-123570390	HMEC	breast:	n/a	n/a
18	CTCF	chr12:123570340-123570490	HCT-116	colon:	n/a	n/a
19	MYC	chr12:123570339-123570635	MCF10A-Er-Src	breast:	n/a	n/a
20	NFIC	chr12:123570232-123570790	SK-N-SH	brain:	n/a	n/a
21	JUND	chr12:123570235-123570727	A549	lung:	n/a	n/a
22	RAD21	chr12:123570322-123570600	A549	lung:	n/a	n/a
23	SP1	chr12:123570054-123570950	HCT-116	colon:	n/a	n/a
24	RFX5	chr12:123570333-123570721	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr12:123570241-123570713	HCT-116	colon:	n/a	n/a
26	POLR2A	chr12:123570301-123570656	HCT-116	colon:	n/a	n/a
27	TCF12	chr12:123570113-123570884	SK-N-SH	brain:	n/a	n/a
28	FOS	chr12:123570236-123570664	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
29	CTCF	chr12:123570320-123570470	RPTEC	kidney:	n/a	n/a
30	FOS	chr12:123570311-123570622	MCF10A-Er-Src	breast:	n/a	chr12:123570448-123570459
31	STAT1	chr12:123570275-123570828	Hela-S3	cervix:	n/a	n/a
32	STAT3	chr12:123570337-123570779	MCF10A-Er-Src	breast:	n/a	chr12:123570533-123570544
33	POLR2A	chr12:123570343-123570584	U87	brain:	n/a	n/a
34	TCF12	chr12:123570143-123570905	A549	lung:	n/a	n/a
35	NR3C1	chr12:123570250-123570722	A549	lung:	n/a	n/a
36	EP300	chr12:123570280-123570680	SK-N-SH_RA	brain:	n/a	n/a
37	NR3C1	chr12:123570288-123570691	A549	lung:	n/a	n/a
38	MAX	chr12:123570339-123570618	Hela-S3	cervix:	n/a	n/a
39	MYC	chr12:123570342-123570697	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr12:123570160-123570944	A549	lung:	n/a	n/a
41	CTCF	chr12:123570320-123570470	A549	lung:	n/a	n/a
42	FOSL2	chr12:123570213-123570642	MCF-7	breast:	n/a	n/a
43	FOSL2	chr12:123570246-123570674	A549	lung:	n/a	n/a
44	CTCF	chr12:123570320-123570470	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr12:123570280-123570430	HEK293	kidney:	n/a	n/a
46	TCF12	chr12:123570197-123570714	SK-N-SH	brain:	n/a	n/a
47	CTCF	chr12:123570300-123570450	HUVEC	blood vessel:	n/a	n/a
48	NFIC	chr12:123570241-123570817	ECC-1	luminal epithelium:	n/a	n/a
49	SMC3	chr12:123570278-123570659	Hela-S3	cervix:	n/a	n/a
50	FOS	chr12:123570236-123570683	HUVEC	blood vessel:	n/a	chr12:123570448-123570459

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
ENSG00000251497	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs4427600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55820451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55992397	0.80[AFR][1000 genomes]
rs56846082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.82[AFR][1000 genomes]
rs58282663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490757	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59995499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60167440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60235187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546720	0.80[AFR][1000 genomes]
rs60894374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61089898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61110645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61396549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.82[AFR][1000 genomes]
rs73411093	0.81[AFR][1000 genomes]
rs73413223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413226	0.82[AFR][1000 genomes]
rs73413228	0.82[AFR][1000 genomes]
rs73413230	0.82[AFR][1000 genomes]
rs73413241	0.82[AFR][1000 genomes]
rs73413246	0.82[AFR][1000 genomes]
rs7964036	0.82[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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123560200-123570400	Weak transcription	Aorta	Aorta
2	chr12:123560600-123574200	Weak transcription	Gastric	stomach
3	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
6	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:123562200-123572600	Weak transcription	K562	blood
8	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
10	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
11	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:123566400-123571600	Enhancers	Right Atrium	heart
13	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:123566600-123571600	Enhancers	Lung	lung
15	chr12:123567200-123570800	Enhancers	Liver	Liver
16	chr12:123567200-123570800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
18	chr12:123567800-123571600	Enhancers	Fetal Muscle Leg	muscle
19	chr12:123568000-123570600	Enhancers	Psoas Muscle	Psoas
20	chr12:123568000-123570800	Enhancers	Fetal Muscle Trunk	muscle
21	chr12:123568000-123571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:123568000-123571400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:123568000-123571400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:123568200-123570800	Enhancers	Stomach Smooth Muscle	stomach
25	chr12:123568200-123571200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:123568200-123571400	Enhancers	Brain Anterior Caudate	brain
27	chr12:123568400-123570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:123568400-123570600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:123568400-123570600	Enhancers	HSMMtube	muscle
30	chr12:123568400-123571000	Enhancers	Primary hematopoietic stem cells	blood
31	chr12:123568400-123571400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:123568400-123571600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:123568600-123570600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:123568600-123571000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
36	chr12:123568800-123571600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:123568800-123571800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:123569000-123570600	Enhancers	GM12878-XiMat	blood
40	chr12:123569000-123570800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:123569000-123574000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:123569200-123570400	Weak transcription	Fetal Brain Female	brain
43	chr12:123569200-123570600	Weak transcription	Adipose Nuclei	Adipose
44	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr12:123569400-123570600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:123569400-123571000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr12:123569400-123571000	Enhancers	Spleen	Spleen
49	chr12:123569400-123574600	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:123569600-123570400	Enhancers	Hela-S3	cervix

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