Variant report

Variant	rs1669919
Chromosome Location	chr12:42877367-42877368
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	POLR2A	chr12:42876627-42877795	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:42875831-42878448	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:42876555-42877703	K562	blood:	n/a	n/a
4	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
5	POLR2A	chr12:42875759-42878501	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr12:42876530-42878610	ECC-1	luminal epithelium:	n/a	n/a
7	EGR1	chr12:42877265-42877573	K562	blood:	n/a	chr12:42877477-42877486 chr12:42877471-42877493 chr12:42877476-42877489 chr12:42877476-42877486
8	RAD21	chr12:42876481-42877604	H1-hESC	embryonic stem cell:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42876706-42876716 chr12:42877442-42877456
9	POLR2A	chr12:42876571-42878212	HUVEC	blood vessel:	n/a	n/a
10	UBTF	chr12:42876624-42878225	K562	blood:	n/a	n/a
11	POLR2A	chr12:42877197-42878492	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr12:42875396-42878400	HUVEC	blood vessel:	n/a	n/a
13	TBP	chr12:42877310-42878710	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:42875592-42878553	HUVEC	blood vessel:	n/a	n/a
15	HMGN3	chr12:42876490-42878160	K562	blood:	n/a	n/a
16	ZNF263	chr12:42876598-42878414	HEK293-T-REx	kidney:	n/a	n/a
17	ZBTB7A	chr12:42876411-42878274	ECC-1	luminal epithelium:	n/a	chr12:42876705-42876714 chr12:42876764-42876773
18	JUND	chr12:42877361-42877614	H1-hESC	embryonic stem cell:	n/a	chr12:42877482-42877491
19	MAX	chr12:42876524-42878434	ECC-1	luminal epithelium:	n/a	n/a
20	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
21	CTCF	chr12:42877280-42877430	GM12872	blood:	n/a	chr12:42877378-42877391
22	CCNT2	chr12:42876491-42878394	K562	blood:	n/a	chr12:42878373-42878393 chr12:42876813-42876822
23	CTCF	chr12:42875902-42878361	SK-N-SH	brain:	n/a	chr12:42877455-42877468 chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42877770-42877783 chr12:42877909-42877922 chr12:42876707-42876717 chr12:42877428-42877441 chr12:42877130-42877143 chr12:42876733-42876746 chr12:42877429-42877439 chr12:42877378-42877391
24	RCOR1	chr12:42876354-42878478	K562	blood:	n/a	n/a
25	TAF7	chr12:42876315-42878323	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:42876675-42878304	IMR90	lung:	n/a	n/a
27	ELF1	chr12:42876559-42877532	GM12878	blood:	n/a	chr12:42876740-42876752 chr12:42876813-42876825 chr12:42876741-42876753 chr12:42876666-42876678 chr12:42877131-42877140
28	MAZ	chr12:42875835-42878737	IMR90	lung:	n/a	n/a
29	FOS	chr12:42877188-42877607	HUVEC	blood vessel:	n/a	chr12:42877253-42877262 chr12:42877482-42877491
30	EP300	chr12:42877293-42878473	ECC-1	luminal epithelium:	n/a	chr12:42878076-42878085 chr12:42877949-42877958 chr12:42877917-42877933 chr12:42877907-42877923 chr12:42877919-42877928 chr12:42877906-42877922 chr12:42877900-42877916
31	ZBTB7A	chr12:42877080-42877777	K562	blood:	n/a	n/a
32	ZBTB7A	chr12:42876498-42877744	K562	blood:	n/a	chr12:42876705-42876714 chr12:42876764-42876773
33	REST	chr12:42876404-42878472	H1-neurons	neurons:	n/a	chr12:42877183-42877196 chr12:42877180-42877193 chr12:42877605-42877625 chr12:42877900-42877910 chr12:42877187-42877196 chr12:42877519-42877532 chr12:42877448-42877461
34	CREB1	chr12:42877321-42877774	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAZ	chr12:42876351-42878358	K562	blood:	n/a	n/a
36	SMC3	chr12:42876282-42878373	SK-N-SH	brain:	n/a	chr12:42876758-42876772 chr12:42876706-42876716 chr12:42876736-42876746
37	ZNF143	chr12:42876579-42877581	GM12878	blood:	n/a	chr12:42877130-42877140 chr12:42877219-42877229
38	POLR2A	chr12:42876530-42878271	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr12:42875748-42878178	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr12:42876763-42877894	ECC-1	luminal epithelium:	n/a	n/a
41	TCF12	chr12:42876391-42878424	ECC-1	luminal epithelium:	n/a	chr12:42877105-42877115 chr12:42877206-42877216
42	POLR2A	chr12:42875836-42878441	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:42876771-42877702	MCF-7	breast:	n/a	n/a
44	RAD21	chr12:42875639-42878864	SK-N-SH	brain:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42877771-42877784 chr12:42876706-42876716 chr12:42877442-42877456 chr12:42876360-42876373
45	CTCF	chr12:42877340-42877490	GM12866	blood:	n/a	chr12:42877455-42877468 chr12:42877428-42877441 chr12:42877429-42877439 chr12:42877378-42877391
46	POLR2A	chr12:42875151-42878403	H1-hESC	embryonic stem cell:	n/a	n/a
47	E2F4	chr12:42876625-42878172	K562	blood:	n/a	chr12:42877219-42877229 chr12:42876664-42876673 chr12:42877451-42877461 chr12:42877939-42877950 chr12:42877944-42877954 chr12:42877128-42877137 chr12:42877426-42877435 chr12:42877923-42877933 chr12:42877908-42877920 chr12:42877129-42877139 chr12:42876665-42876675
48	POLR2A	chr12:42876468-42877818	HUVEC	blood vessel:	n/a	n/a
49	SIN3A	chr12:42875185-42878606	H1-hESC	embryonic stem cell:	n/a	chr12:42877917-42877930 chr12:42877519-42877532 chr12:42877448-42877461 chr12:42877569-42877580 chr12:42877192-42877203 chr12:42877183-42877196
50	TCF7L2	chr12:42876620-42878337	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
PRICKLE1	TF binding region

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1626507	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1669920	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2600937	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2708070	0.88[AFR][1000 genomes];1.00[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	chr12:42875800-42878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:42875800-42878600	Active TSS	Ovary	ovary
8	chr12:42875800-42878600	Active TSS	Right Atrium	heart
9	chr12:42875800-42878600	Active TSS	Right Ventricle	heart
10	chr12:42876000-42877400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:42876000-42877800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
12	chr12:42876000-42878000	Active TSS	NHDF-Ad	bronchial
13	chr12:42876000-42878200	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:42876000-42878200	Active TSS	Brain Angular Gyrus	brain
15	chr12:42876000-42878200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr12:42876000-42878200	Active TSS	Lung	lung
17	chr12:42876000-42878200	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:42876000-42878400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:42876000-42878400	Active TSS	Colon Smooth Muscle	Colon
20	chr12:42876000-42878400	Active TSS	Rectal Smooth Muscle	rectum
21	chr12:42876000-42878600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:42876000-42878600	Active TSS	Aorta	Aorta
23	chr12:42876200-42877600	Active TSS	Fetal Intestine Small	intestine
24	chr12:42876200-42878000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:42876200-42878200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:42876200-42878200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
27	chr12:42876200-42878200	Active TSS	Duodenum Mucosa	Duodenum
28	chr12:42876200-42878200	Active TSS	Gastric	stomach
29	chr12:42876200-42878200	Active TSS	NH-A	brain
30	chr12:42876200-42878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr12:42876200-42878400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:42876200-42878400	Active TSS	Fetal Kidney	kidney
33	chr12:42876200-42878400	Active TSS	Left Ventricle	heart
34	chr12:42876200-42878600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr12:42876400-42877800	Flanking Active TSS	Liver	Liver
36	chr12:42876400-42878000	Active TSS	Esophagus	oesophagus
37	chr12:42876400-42878200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:42876400-42878200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr12:42876400-42878200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr12:42876400-42878200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
41	chr12:42876400-42878200	Active TSS	Brain Anterior Caudate	brain
42	chr12:42876400-42878200	Active TSS	Brain Substantia Nigra	brain
43	chr12:42876400-42878200	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr12:42876400-42878200	Active TSS	Fetal Lung	lung
45	chr12:42876400-42878200	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr12:42876400-42878200	Active TSS	HSMM	muscle
47	chr12:42876400-42878200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
48	chr12:42876400-42878400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:42876400-42878400	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:42876400-42878400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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