Variant report

Variant	rs4499062
Chromosome Location	chr12:42877861-42877862
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	HA-E2F1	chr12:42877403-42878360	MCF-7	breast:	n/a	chr12:42877451-42877461 chr12:42877944-42877954 chr12:42877426-42877435 chr12:42877923-42877933 chr12:42877908-42877920
2	ELF1	chr12:42877861-42878174	K562	blood:	n/a	chr12:42877942-42877954 chr12:42877946-42877955
3	MAX	chr12:42877645-42878429	A549	lung:	n/a	n/a
4	E2F4	chr12:42877766-42878490	MCF10A-Er-Src	breast:	n/a	chr12:42877939-42877950 chr12:42877944-42877954 chr12:42877923-42877933 chr12:42877908-42877920
5	ZBTB7A	chr12:42877805-42878189	K562	blood:	n/a	n/a
6	MAX	chr12:42877699-42878328	A549	lung:	n/a	n/a
7	POLR2A	chr12:42875831-42878448	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr12:42877530-42877940	K562	blood:	n/a	n/a
9	E2F6	chr12:42877835-42878075	K562	blood:	n/a	chr12:42877944-42877954 chr12:42877923-42877933 chr12:42877908-42877920
10	POLR2A	chr12:42875759-42878501	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr12:42877648-42878000	K562	blood:	n/a	chr12:42877770-42877783 chr12:42877909-42877922
12	MAZ	chr12:42877856-42878028	HepG2	liver:	n/a	n/a
13	MAX	chr12:42876530-42878610	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr12:42877561-42878468	HCT-116	colon:	n/a	n/a
15	ELF1	chr12:42877792-42878146	GM12878	blood:	n/a	chr12:42877942-42877954 chr12:42877946-42877955
16	POLR2A	chr12:42876571-42878212	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr12:42877851-42878033	MCF-7	breast:	n/a	chr12:42877909-42877922
18	MAX	chr12:42877860-42878407	H1-hESC	embryonic stem cell:	n/a	n/a
19	STAT3	chr12:42877805-42878310	MCF10A-Er-Src	breast:	n/a	chr12:42877960-42877969 chr12:42877959-42877968 chr12:42877957-42877971
20	HCFC1	chr12:42877562-42878230	K562	blood:	n/a	n/a
21	UBTF	chr12:42876624-42878225	K562	blood:	n/a	n/a
22	POLR2A	chr12:42877197-42878492	H1-neurons	neurons:	n/a	n/a
23	BHLHE40	chr12:42877808-42878286	HepG2	liver:	n/a	chr12:42877939-42877955 chr12:42877907-42877923
24	HDAC2	chr12:42877750-42878512	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:42875396-42878400	HUVEC	blood vessel:	n/a	n/a
26	CREB1	chr12:42877778-42878550	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr12:42877818-42878401	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBP	chr12:42877310-42878710	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:42875592-42878553	HUVEC	blood vessel:	n/a	n/a
30	MAX	chr12:42877789-42878220	K562	blood:	n/a	n/a
31	EP300	chr12:42877766-42878487	H1-hESC	embryonic stem cell:	n/a	chr12:42878076-42878085 chr12:42877949-42877958 chr12:42877917-42877933 chr12:42877907-42877923 chr12:42877919-42877928 chr12:42877906-42877922 chr12:42877900-42877916
32	CTCF	chr12:42877800-42877950	A549	lung:	n/a	chr12:42877909-42877922
33	CTCF	chr12:42877780-42877930	RPTEC	kidney:	n/a	chr12:42877909-42877922
34	HMGN3	chr12:42876490-42878160	K562	blood:	n/a	n/a
35	CTCF	chr12:42877840-42877990	SK-N-SH_RA	brain:	n/a	chr12:42877909-42877922
36	RAD21	chr12:42877612-42878431	H1-hESC	embryonic stem cell:	n/a	chr12:42877771-42877784
37	ZNF263	chr12:42876598-42878414	HEK293-T-REx	kidney:	n/a	n/a
38	RAD21	chr12:42877544-42878270	IMR90	lung:	n/a	chr12:42877771-42877784
39	TAF1	chr12:42877845-42878319	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOXA2	chr12:42877732-42878321	A549	lung:	n/a	n/a
41	ZBTB7A	chr12:42876411-42878274	ECC-1	luminal epithelium:	n/a	chr12:42876705-42876714 chr12:42876764-42876773
42	MAX	chr12:42876524-42878434	ECC-1	luminal epithelium:	n/a	n/a
43	JUND	chr12:42877809-42878268	K562	blood:	n/a	chr12:42878077-42878086
44	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
45	MAX	chr12:42877837-42878294	K562	blood:	n/a	n/a
46	POLR2A	chr12:42877847-42878306	H1-hESC	embryonic stem cell:	n/a	n/a
47	CCNT2	chr12:42876491-42878394	K562	blood:	n/a	chr12:42878373-42878393 chr12:42876813-42876822
48	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
49	RCOR1	chr12:42876354-42878478	K562	blood:	n/a	n/a
50	CTCF	chr12:42877482-42877990	IMR90	lung:	n/a	chr12:42877770-42877783 chr12:42877909-42877922

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12427122	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12823141	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2141931	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55962740	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73128403	0.95[AMR][1000 genomes];0.89[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42875400-42878600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:42875400-42878800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:42875400-42878800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:42875400-42878800	Active TSS	NHLF	lung
5	chr12:42875800-42878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:42875800-42878600	Active TSS	Ovary	ovary
7	chr12:42875800-42878600	Active TSS	Right Atrium	heart
8	chr12:42875800-42878600	Active TSS	Right Ventricle	heart
9	chr12:42876000-42878000	Active TSS	NHDF-Ad	bronchial
10	chr12:42876000-42878200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr12:42876000-42878200	Active TSS	Brain Angular Gyrus	brain
12	chr12:42876000-42878200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr12:42876000-42878200	Active TSS	Lung	lung
14	chr12:42876000-42878200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:42876000-42878400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:42876000-42878400	Active TSS	Colon Smooth Muscle	Colon
17	chr12:42876000-42878400	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:42876000-42878600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:42876000-42878600	Active TSS	Aorta	Aorta
20	chr12:42876200-42878000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:42876200-42878200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:42876200-42878200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr12:42876200-42878200	Active TSS	Duodenum Mucosa	Duodenum
24	chr12:42876200-42878200	Active TSS	Gastric	stomach
25	chr12:42876200-42878200	Active TSS	NH-A	brain
26	chr12:42876200-42878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr12:42876200-42878400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:42876200-42878400	Active TSS	Fetal Kidney	kidney
29	chr12:42876200-42878400	Active TSS	Left Ventricle	heart
30	chr12:42876200-42878600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr12:42876400-42878000	Active TSS	Esophagus	oesophagus
32	chr12:42876400-42878200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:42876400-42878200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr12:42876400-42878200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:42876400-42878200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr12:42876400-42878200	Active TSS	Brain Anterior Caudate	brain
37	chr12:42876400-42878200	Active TSS	Brain Substantia Nigra	brain
38	chr12:42876400-42878200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:42876400-42878200	Active TSS	Fetal Lung	lung
40	chr12:42876400-42878200	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:42876400-42878200	Active TSS	HSMM	muscle
42	chr12:42876400-42878200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
43	chr12:42876400-42878400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:42876400-42878400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:42876400-42878400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:42876400-42878400	Active TSS	Osteobl	bone
47	chr12:42876400-42878600	Active TSS	Fetal Muscle Trunk	muscle
48	chr12:42876400-42878600	Active TSS	Psoas Muscle	Psoas
49	chr12:42876400-42878800	Active TSS	Stomach Smooth Muscle	stomach
50	chr12:42876600-42878000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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