Variant report

Variant	rs560478560
Chromosome Location	chr12:42983926-42983927
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	TCF12	chr12:42982660-42984155	ECC-1	luminal epithelium:	n/a	chr12:42982744-42982753 chr12:42983785-42983795
2	POLR2A	chr12:42983088-42983936	HUVEC	blood vessel:	n/a	n/a
3	CTBP2	chr12:42982768-42984725	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr12:42982100-42984824	IMR90	lung:	n/a	chr12:42984253-42984268
5	EGR1	chr12:42983432-42983931	ECC-1	luminal epithelium:	n/a	chr12:42983667-42983681 chr12:42983870-42983880 chr12:42983668-42983681 chr12:42983668-42983681 chr12:42983669-42983679 chr12:42983663-42983685
6	RAD21	chr12:42982104-42984161	IMR90	lung:	n/a	chr12:42983223-42983235 chr12:42982867-42982886
7	EP300	chr12:42982235-42984855	ECC-1	luminal epithelium:	n/a	chr12:42982351-42982361 chr12:42983501-42983510 chr12:42983498-42983507 chr12:42984759-42984773
8	GATA2	chr12:42983633-42984242	HUVEC	blood vessel:	n/a	n/a
9	NFIC	chr12:42982719-42984696	ECC-1	luminal epithelium:	n/a	n/a
10	RAD21	chr12:42983717-42984052	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr12:42983191-42984783	ECC-1	luminal epithelium:	n/a	n/a
12	YY1	chr12:42983181-42984115	ECC-1	luminal epithelium:	n/a	chr12:42983496-42983505 chr12:42983634-42983648 chr12:42983499-42983508 chr12:42983218-42983229 chr12:42983499-42983513 chr12:42983639-42983648 chr12:42983871-42983880 chr12:42983496-42983510 chr12:42983512-42983526
13	POLR2A	chr12:42983362-42984548	MCF10A-Er-Src	breast:	n/a	n/a
14	TEAD4	chr12:42983012-42984809	ECC-1	luminal epithelium:	n/a	n/a
15	MAX	chr12:42983324-42983962	A549	lung:	n/a	chr12:42983670-42983679
16	MAZ	chr12:42981376-42985082	IMR90	lung:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
17	ZNF384	chr12:42983523-42984226	K562	blood:	n/a	n/a
18	RAD21	chr12:42982653-42983952	ECC-1	luminal epithelium:	n/a	chr12:42983223-42983235 chr12:42982867-42982886
19	MAX	chr12:42982660-42984847	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
20	ZNF263	chr12:42981422-42984401	HEK293-T-REx	kidney:	n/a	chr12:42982475-42982496
21	POLR2A	chr12:42983212-42984624	HUVEC	blood vessel:	n/a	n/a
22	REST	chr12:42981515-42984211	H1-neurons	neurons:	n/a	chr12:42983762-42983775 chr12:42983222-42983235
23	EGR1	chr12:42983436-42983979	ECC-1	luminal epithelium:	n/a	chr12:42983963-42983976 chr12:42983667-42983681 chr12:42983870-42983880 chr12:42983668-42983681 chr12:42983668-42983681 chr12:42983669-42983679 chr12:42983663-42983685
24	MYC	chr12:42983516-42983940	MCF10A-Er-Src	breast:	n/a	chr12:42983670-42983679
25	SMC3	chr12:42982437-42984934	SK-N-SH	brain:	n/a	chr12:42982812-42982819 chr12:42984593-42984607 chr12:42982868-42982882
26	RAD21	chr12:42981077-42985218	SK-N-SH	brain:	n/a	chr12:42983223-42983235 chr12:42982867-42982886 chr12:42984597-42984607 chr12:42984597-42984609
27	TAF1	chr12:42982944-42984815	ECC-1	luminal epithelium:	n/a	n/a
28	RAD21	chr12:42982584-42983965	H1-hESC	embryonic stem cell:	n/a	chr12:42983223-42983235 chr12:42982867-42982886
29	TAF1	chr12:42983032-42984604	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr12:42983361-42984689	MCF10A-Er-Src	breast:	n/a	n/a
31	MAX	chr12:42982586-42984897	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
32	POLR2A	chr12:42983277-42983983	HUVEC	blood vessel:	n/a	n/a
33	MXI1	chr12:42980685-42985161	SK-N-SH	brain:	n/a	chr12:42984253-42984268
34	SIN3AK20	chr12:42983132-42983930	PANC-1	pancreas:	n/a	n/a
35	RAD21	chr12:42983860-42984800	H1-hESC	embryonic stem cell:	n/a	chr12:42984597-42984607 chr12:42984597-42984609
36	ZBTB7A	chr12:42982586-42984766	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr12:42983017-42984199	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr12:42980860-42984627	HUVEC	blood vessel:	n/a	n/a
39	MAX	chr12:42982680-42984684	A549	lung:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
40	POLR2A	chr12:42982765-42984752	ECC-1	luminal epithelium:	n/a	n/a
41	RAD21	chr12:42983350-42984083	SK-N-SH_RA	brain:	n/a	n/a
42	KAP1	chr12:42983881-42984910	HEK293	kidney:	n/a	n/a
43	SIN3A	chr12:42982670-42984829	H1-hESC	embryonic stem cell:	n/a	chr12:42983657-42983668 chr12:42983657-42983670
44	ZBTB7A	chr12:42983585-42984809	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv989438	chr12:42981066-42988699	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3361465	chr12:42982310-42984858	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3339962	chr12:42982685-42984683	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42980000-42985000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:42980600-42984200	Active TSS	HSMMtube	muscle
3	chr12:42980800-42984200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:42981000-42984000	Active TSS	Brain Angular Gyrus	brain
5	chr12:42981000-42984000	Active TSS	Fetal Muscle Leg	muscle
6	chr12:42981200-42984000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:42981200-42985000	Active TSS	Right Atrium	heart
8	chr12:42981400-42984000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:42981400-42984000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr12:42981400-42984200	Active TSS	Brain Anterior Caudate	brain
11	chr12:42981400-42984800	Active TSS	Right Ventricle	heart
12	chr12:42981600-42984200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:42981600-42984400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr12:42981600-42985000	Active TSS	Fetal Kidney	kidney
15	chr12:42981800-42984600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:42981800-42984800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr12:42982000-42984000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:42982000-42984000	Bivalent/Poised TSS	Colonic Mucosa	Colon
19	chr12:42982000-42984000	Active TSS	HSMM	muscle
20	chr12:42982000-42984000	Active TSS	HUVEC	blood vessel
21	chr12:42982000-42984000	Active TSS	NH-A	brain
22	chr12:42982000-42984800	Active TSS	Aorta	Aorta
23	chr12:42982000-42984800	Active TSS	Left Ventricle	heart
24	chr12:42982000-42984800	Active TSS	Ovary	ovary
25	chr12:42982000-42985000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:42982200-42984000	Active TSS	Fetal Lung	lung
27	chr12:42982200-42984000	Active TSS	HMEC	breast
28	chr12:42982200-42984000	Active TSS	Osteobl	bone
29	chr12:42982200-42984200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:42982200-42984400	Active TSS	Rectal Smooth Muscle	rectum
31	chr12:42982400-42984200	Active TSS	Colon Smooth Muscle	Colon
32	chr12:42982400-42984200	Active TSS	Lung	lung
33	chr12:42982400-42984200	Active TSS	Stomach Smooth Muscle	stomach
34	chr12:42982400-42984400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:42982400-42984400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:42982400-42984400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:42982400-42984600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:42982400-42984800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:42982400-42984800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:42982400-42984800	Active TSS	Psoas Muscle	Psoas
41	chr12:42982600-42984000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
42	chr12:42982600-42984000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr12:42982600-42984000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:42982600-42984000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:42982600-42984000	Active TSS	NHEK	skin
46	chr12:42982600-42984200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr12:42982600-42984200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
48	chr12:42982600-42984200	Active TSS	Spleen	Spleen
49	chr12:42982600-42984400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:42982600-42984400	Bivalent/Poised TSS	A549	lung

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