Variant report

Variant	rs12823141
Chromosome Location	chr12:42876965-42876966
allele	G/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	RAD21	chr12:42876492-42877047	MCF-7	breast:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
2	MAX	chr12:42876448-42877295	A549	lung:	n/a	n/a
3	TAF1	chr12:42876754-42877160	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr12:42876627-42877795	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:42875831-42878448	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr12:42876555-42877703	K562	blood:	n/a	n/a
7	POLR2A	chr12:42876505-42877177	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr12:42876506-42877672	GM12878	blood:	n/a	chr12:42877455-42877468 chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42877428-42877441 chr12:42877130-42877143 chr12:42876733-42876746 chr12:42877429-42877439 chr12:42877378-42877391
9	CTCF	chr12:42876369-42877111	K562	blood:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
10	CTCF	chr12:42876959-42876992	GM19240	blood:	n/a	n/a
11	MAX	chr12:42876571-42877237	A549	lung:	n/a	n/a
12	POLR2A	chr12:42875759-42878501	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr12:42876530-42878610	ECC-1	luminal epithelium:	n/a	n/a
14	RFX5	chr12:42876773-42877021	GM12878	blood:	n/a	n/a
15	RAD21	chr12:42876588-42876997	HepG2	liver:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
16	TBP	chr12:42876561-42877046	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr12:42876493-42877030	SK-N-SH_RA	brain:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
18	BACH1	chr12:42876321-42876965	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr12:42876509-42876974	H1-hESC	embryonic stem cell:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
20	SIN3AK20	chr12:42876546-42877097	PANC-1	pancreas:	n/a	n/a
21	RAD21	chr12:42876481-42877604	H1-hESC	embryonic stem cell:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716 chr12:42877442-42877456
22	YY1	chr12:42876646-42877356	ECC-1	luminal epithelium:	n/a	chr12:42876739-42876753 chr12:42876664-42876673 chr12:42877296-42877307 chr12:42876664-42876675 chr12:42877256-42877270 chr12:42877215-42877229 chr12:42877128-42877137 chr12:42876739-42876748 chr12:42877129-42877143
23	SMC3	chr12:42876551-42877017	GM12878	blood:	n/a	chr12:42876758-42876772 chr12:42876706-42876716 chr12:42876736-42876746
24	CTCF	chr12:42876511-42876977	HepG2	liver:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
25	POLR2A	chr12:42876571-42878212	HUVEC	blood vessel:	n/a	n/a
26	CTCF	chr12:42876578-42877082	GM19239	blood:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
27	UBTF	chr12:42876624-42878225	K562	blood:	n/a	n/a
28	E2F6	chr12:42876570-42877247	A549	lung:	n/a	chr12:42877219-42877229 chr12:42876664-42876673 chr12:42877128-42877137 chr12:42877129-42877139 chr12:42876665-42876675
29	CTCF	chr12:42876330-42877243	HCT-116	colon:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42877130-42877143 chr12:42876733-42876746
30	POLR2A	chr12:42875396-42878400	HUVEC	blood vessel:	n/a	n/a
31	FOXM1	chr12:42876418-42877054	GM12878	blood:	n/a	n/a
32	CTCF	chr12:42876482-42876973	K562	blood:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
33	MYC	chr12:42876390-42877124	K562	blood:	n/a	n/a
34	POLR2A	chr12:42875592-42878553	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr12:42876383-42877084	MCF-7	breast:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
36	YY1	chr12:42876545-42877044	HepG2	liver:	n/a	chr12:42876739-42876753 chr12:42876664-42876673 chr12:42876664-42876675 chr12:42876739-42876748
37	CTCF	chr12:42876369-42877145	HCT-116	colon:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42877130-42877143 chr12:42876733-42876746
38	ATF2	chr12:42876501-42877046	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr12:42876492-42876991	A549	lung:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
40	CTCF	chr12:42876596-42877085	MCF-7	breast:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
41	CTCF	chr12:42876562-42877013	Gliobla	brain:	n/a	chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42876707-42876717 chr12:42876733-42876746
42	RAD21	chr12:42876316-42877161	IMR90	lung:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716 chr12:42876360-42876373
43	HMGN3	chr12:42876490-42878160	K562	blood:	n/a	n/a
44	ZNF263	chr12:42876598-42878414	HEK293-T-REx	kidney:	n/a	n/a
45	RAD21	chr12:42876389-42877210	A549	lung:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716
46	ZBTB7A	chr12:42876411-42878274	ECC-1	luminal epithelium:	n/a	chr12:42876705-42876714 chr12:42876764-42876773
47	MAX	chr12:42876524-42878434	ECC-1	luminal epithelium:	n/a	n/a
48	RAD21	chr12:42876352-42877206	HCT-116	colon:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716 chr12:42876360-42876373
49	CCNT2	chr12:42876491-42878394	K562	blood:	n/a	chr12:42878373-42878393 chr12:42876813-42876822
50	RAD21	chr12:42876595-42877053	ECC-1	luminal epithelium:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12423597	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12427122	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812683	1.00[ASN][1000 genomes]
rs2141931	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34290145	1.00[ASN][1000 genomes]
rs4499062	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55962740	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59323847	0.83[EUR][1000 genomes]
rs73128403	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][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	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42875000-42877800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:42875400-42878600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:42875400-42878800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:42875400-42878800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:42875400-42878800	Active TSS	NHLF	lung
6	chr12:42875800-42877200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:42875800-42878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:42875800-42878600	Active TSS	Ovary	ovary
9	chr12:42875800-42878600	Active TSS	Right Atrium	heart
10	chr12:42875800-42878600	Active TSS	Right Ventricle	heart
11	chr12:42876000-42877400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:42876000-42877800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
13	chr12:42876000-42878000	Active TSS	NHDF-Ad	bronchial
14	chr12:42876000-42878200	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:42876000-42878200	Active TSS	Brain Angular Gyrus	brain
16	chr12:42876000-42878200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr12:42876000-42878200	Active TSS	Lung	lung
18	chr12:42876000-42878200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:42876000-42878400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:42876000-42878400	Active TSS	Colon Smooth Muscle	Colon
21	chr12:42876000-42878400	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:42876000-42878600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr12:42876000-42878600	Active TSS	Aorta	Aorta
24	chr12:42876200-42877000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr12:42876200-42877000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:42876200-42877600	Active TSS	Fetal Intestine Small	intestine
27	chr12:42876200-42878000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:42876200-42878200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:42876200-42878200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr12:42876200-42878200	Active TSS	Duodenum Mucosa	Duodenum
31	chr12:42876200-42878200	Active TSS	Gastric	stomach
32	chr12:42876200-42878200	Active TSS	NH-A	brain
33	chr12:42876200-42878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:42876200-42878400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:42876200-42878400	Active TSS	Fetal Kidney	kidney
36	chr12:42876200-42878400	Active TSS	Left Ventricle	heart
37	chr12:42876200-42878600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:42876400-42877000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:42876400-42877200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:42876400-42877200	Active TSS	Placenta	Placenta
41	chr12:42876400-42877200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr12:42876400-42877800	Flanking Active TSS	Liver	Liver
43	chr12:42876400-42878000	Active TSS	Esophagus	oesophagus
44	chr12:42876400-42878200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:42876400-42878200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:42876400-42878200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr12:42876400-42878200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr12:42876400-42878200	Active TSS	Brain Anterior Caudate	brain
49	chr12:42876400-42878200	Active TSS	Brain Substantia Nigra	brain
50	chr12:42876400-42878200	Active TSS	Pancreatic Islets	Pancreatic Islet

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