Variant report

Variant	rs60809882
Chromosome Location	chr12:123519742-123519743
allele	A/C
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	FOSL2	chr12:123519390-123519872	A549	lung:	n/a	chr12:123519699-123519708
2	GATA3	chr12:123519422-123520088	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr12:123519487-123519815	IMR90	lung:	n/a	chr12:123519665-123519679
4	CTCF	chr12:123519640-123519790	HCFaa	heart:	n/a	n/a
5	CTCF	chr12:123519680-123519830	HRPEpiC	eye:	n/a	n/a
6	NR3C1	chr12:123519205-123519761	A549	lung:	n/a	chr12:123519520-123519534 chr12:123519250-123519276 chr12:123519251-123519258 chr12:123519519-123519535 chr12:123519514-123519540 chr12:123519514-123519540 chr12:123519243-123519252
7	EBF1	chr12:123519584-123519765	GM12878	blood:	n/a	chr12:123519711-123519722
8	POLR2A	chr12:123519387-123519888	H1-neurons	neurons:	n/a	n/a
9	CTCF	chr12:123519600-123519750	AG04450	lung:	n/a	n/a
10	CTCF	chr12:123519600-123519750	HEK293	kidney:	n/a	n/a
11	CTCF	chr12:123519620-123519770	AG10803	skin:	n/a	n/a
12	FOS	chr12:123519564-123519763	MCF10A-Er-Src	breast:	n/a	chr12:123519699-123519708
13	CTCF	chr12:123519640-123519790	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr12:123519600-123519750	WI-38	lung:	n/a	n/a
15	PBX3	chr12:123519403-123519959	SK-N-SH	brain:	n/a	n/a
16	KAP1	chr12:123519345-123519908	U2OS	brain:	n/a	n/a
17	EP300	chr12:123519473-123519779	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr12:123519600-123519750	HBMEC	blood vessel:	n/a	n/a
19	PBX3	chr12:123519376-123519952	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr12:123519640-123519790	HBMEC	blood vessel:	n/a	n/a
21	NR3C1	chr12:123519209-123519869	A549	lung:	n/a	chr12:123519520-123519534 chr12:123519250-123519276 chr12:123519251-123519258 chr12:123519519-123519535 chr12:123519514-123519540 chr12:123519514-123519540 chr12:123519243-123519252
22	NR3C1	chr12:123519293-123519797	A549	lung:	n/a	chr12:123519520-123519534 chr12:123519519-123519535 chr12:123519514-123519540 chr12:123519514-123519540
23	NR3C1	chr12:123519311-123519754	A549	lung:	n/a	chr12:123519520-123519534 chr12:123519519-123519535 chr12:123519514-123519540 chr12:123519514-123519540
24	RAD21	chr12:123519501-123519778	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr12:123519680-123519830	AG04450	lung:	n/a	n/a
26	JUND	chr12:123519561-123519787	HepG2	liver:	n/a	chr12:123519699-123519708

No.	Distal block	Cell Line	Cell type
1	chr12:123519450..123520015-chr12:123547209..123548090,3	MCF-7	breast:
2	chr12:123519670..123521878-chr12:123527130..123529862,2	MCF-7	breast:
3	chr12:123519450..123519972-chr12:123547209..123548024,2	MCF-7	breast:

Variant related genes	Relation type
PITPNM2	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11061578	1.00[AFR][1000 genomes]
rs34010146	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55646110	0.85[AMR][1000 genomes]
rs55796417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55813219	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55830208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55939945	0.85[AMR][1000 genomes]
rs55951195	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55992397	0.89[AFR][1000 genomes]
rs56000615	0.85[AMR][1000 genomes]
rs56020503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56140750	0.97[AFR][1000 genomes]
rs56150478	1.00[AMR][1000 genomes]
rs56288804	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56725866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57106451	1.00[AFR][1000 genomes]
rs57110420	0.85[AMR][1000 genomes]
rs57178349	0.91[AFR][1000 genomes]
rs57258703	0.85[AMR][1000 genomes]
rs57641050	1.00[AFR][1000 genomes]
rs57764857	1.00[AFR][1000 genomes]
rs57794792	1.00[AFR][1000 genomes]
rs57863319	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58025094	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58462666	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59081274	0.85[AMR][1000 genomes]
rs59211448	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59379557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59526938	0.85[AMR][1000 genomes]
rs59615440	0.90[AFR][1000 genomes]
rs60341839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60341983	0.97[AFR][1000 genomes]
rs60358140	1.00[AFR][1000 genomes]
rs60546720	0.89[AFR][1000 genomes]
rs60739634	0.85[AMR][1000 genomes]
rs60761837	0.83[AFR][1000 genomes]
rs60888713	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60901287	0.85[AMR][1000 genomes]
rs60920158	1.00[AMR][1000 genomes]
rs60987910	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61061591	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61377358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61516893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61546241	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61592192	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61677786	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7295258	0.85[AMR][1000 genomes]
rs73406966	1.00[AMR][1000 genomes]
rs73406997	1.00[AMR][1000 genomes]
rs73408803	1.00[AMR][1000 genomes]
rs73408810	1.00[AMR][1000 genomes]
rs73408812	1.00[AMR][1000 genomes]
rs73408818	0.85[AMR][1000 genomes]
rs73408820	0.85[AMR][1000 genomes]
rs73408832	0.85[AMR][1000 genomes]
rs73408835	0.85[AMR][1000 genomes]
rs73408838	1.00[AMR][1000 genomes]
rs73408846	1.00[AMR][1000 genomes]
rs73408887	1.00[AMR][1000 genomes]
rs73408890	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73408892	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73408893	0.85[AMR][1000 genomes]
rs73408894	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73408899	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411006	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411009	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411011	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411014	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411015	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411017	1.00[AMR][1000 genomes]
rs73411018	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411027	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73411033	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411041	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411043	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411076	1.00[AFR][1000 genomes]
rs73411084	0.90[AFR][1000 genomes]
rs73411087	0.97[AFR][1000 genomes]
rs73411088	0.87[AFR][1000 genomes]
rs73411090	0.91[AFR][1000 genomes]
rs73411093	0.90[AFR][1000 genomes]
rs73411098	0.83[AFR][1000 genomes]
rs73413226	0.91[AFR][1000 genomes]
rs73413228	0.91[AFR][1000 genomes]
rs73413230	0.91[AFR][1000 genomes]
rs73413236	0.89[AFR][1000 genomes]
rs73413241	0.91[AFR][1000 genomes]
rs73413246	0.91[AFR][1000 genomes]
rs73413265	0.81[AFR][1000 genomes]
rs752164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7952760	0.97[AFR][1000 genomes]
rs7964036	0.91[AFR][1000 genomes]
rs7971535	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	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
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
2	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:123491600-123526400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:123496000-123526400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:123497400-123528600	Weak transcription	Ovary	ovary
6	chr12:123497800-123526000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:123504200-123528000	Weak transcription	HMEC	breast
8	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
9	chr12:123507400-123526000	Genic enhancers	Fetal Thymus	thymus
10	chr12:123509800-123525600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:123511400-123528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:123515600-123521600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:123516400-123527400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:123516600-123527800	Weak transcription	Stomach Mucosa	stomach
16	chr12:123517200-123521800	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:123517400-123520600	Enhancers	K562	blood
18	chr12:123517600-123519800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:123517800-123519800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:123517800-123526800	Weak transcription	Fetal Heart	heart
21	chr12:123517800-123527200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:123518000-123519800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:123518000-123526400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:123518200-123519800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:123518200-123527600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:123518200-123528000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:123518200-123535600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:123518400-123520000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123518400-123527200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:123518400-123527200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:123518400-123533600	Weak transcription	Aorta	Aorta
32	chr12:123518600-123520000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:123518600-123520000	Enhancers	NHDF-Ad	bronchial
34	chr12:123518800-123520000	Enhancers	NH-A	brain
35	chr12:123518800-123520600	Weak transcription	Brain Germinal Matrix	brain
36	chr12:123518800-123526000	Weak transcription	Placenta	Placenta
37	chr12:123518800-123526400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:123518800-123527400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:123518800-123528200	Weak transcription	Brain Substantia Nigra	brain
40	chr12:123518800-123540600	Weak transcription	HepG2	liver
41	chr12:123519000-123519800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:123519000-123519800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:123519000-123519800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:123519000-123519800	Enhancers	A549	lung
45	chr12:123519000-123520000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:123519000-123520000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:123519000-123520000	Enhancers	Adipose Nuclei	Adipose
48	chr12:123519000-123524400	Genic enhancers	Thymus	Thymus
49	chr12:123519000-123526200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:123519000-123526400	Weak transcription	Pancreas	Pancrea

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