Variant report

Variant	rs2708070
Chromosome Location	chr12:42878328-42878329
allele	A/G
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	MAX	chr12:42877645-42878429	A549	lung:	n/a	n/a
3	E2F4	chr12:42877766-42878490	MCF10A-Er-Src	breast:	n/a	chr12:42877939-42877950 chr12:42877944-42877954 chr12:42877923-42877933 chr12:42877908-42877920
4	EP300	chr12:42878078-42878448	H1-hESC	embryonic stem cell:	n/a	n/a
5	ATF2	chr12:42877896-42878546	H1-hESC	embryonic stem cell:	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	SP1	chr12:42878019-42878556	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr12:42877937-42878470	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr12:42878103-42878406	H1-hESC	embryonic stem cell:	n/a	chr12:42878251-42878267
11	POLR2A	chr12:42875759-42878501	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr12:42876530-42878610	ECC-1	luminal epithelium:	n/a	n/a
13	YY1	chr12:42877870-42878361	H1-hESC	embryonic stem cell:	n/a	chr12:42877916-42877930 chr12:42877941-42877955 chr12:42877928-42877942 chr12:42877905-42877916 chr12:42877946-42877955
14	MAX	chr12:42877561-42878468	HCT-116	colon:	n/a	n/a
15	MAX	chr12:42877860-42878407	H1-hESC	embryonic stem cell:	n/a	n/a
16	EBF1	chr12:42878251-42878388	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:42877197-42878492	H1-neurons	neurons:	n/a	n/a
18	TEAD4	chr12:42877931-42878506	H1-hESC	embryonic stem cell:	n/a	n/a
19	HDAC2	chr12:42877750-42878512	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:42875396-42878400	HUVEC	blood vessel:	n/a	n/a
21	CREB1	chr12:42877778-42878550	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr12:42877818-42878401	H1-hESC	embryonic stem cell:	n/a	n/a
23	TBP	chr12:42877310-42878710	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUN	chr12:42877956-42878372	H1-hESC	embryonic stem cell:	n/a	chr12:42878077-42878086
25	FOXA1	chr12:42877897-42878354	T-47D	breast:	n/a	n/a
26	POLR2A	chr12:42875592-42878553	HUVEC	blood vessel:	n/a	n/a
27	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
28	CEBPB	chr12:42877896-42878457	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr12:42877612-42878431	H1-hESC	embryonic stem cell:	n/a	chr12:42877771-42877784
30	ZNF263	chr12:42876598-42878414	HEK293-T-REx	kidney:	n/a	n/a
31	FOS	chr12:42878309-42878514	MCF10A-Er-Src	breast:	n/a	n/a
32	POU5F1	chr12:42877927-42878479	H1-hESC	embryonic stem cell:	n/a	chr12:42878301-42878309 chr12:42878301-42878315 chr12:42878301-42878315 chr12:42878300-42878314 chr12:42878301-42878315
33	MYC	chr12:42877985-42878424	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr12:42876524-42878434	ECC-1	luminal epithelium:	n/a	n/a
35	MYC	chr12:42878131-42878537	MCF10A-Er-Src	breast:	n/a	n/a
36	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
37	CCNT2	chr12:42876491-42878394	K562	blood:	n/a	chr12:42878373-42878393 chr12:42876813-42876822
38	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
39	BHLHE40	chr12:42878002-42878456	GM12878	blood:	n/a	n/a
40	RCOR1	chr12:42876354-42878478	K562	blood:	n/a	n/a
41	KAP1	chr12:42877878-42879180	HEK293	kidney:	n/a	n/a
42	TEAD4	chr12:42877805-42878427	ECC-1	luminal epithelium:	n/a	n/a
43	NANOG	chr12:42877866-42878459	H1-hESC	embryonic stem cell:	n/a	n/a
44	BCL11A	chr12:42878103-42878363	H1-hESC	embryonic stem cell:	n/a	chr12:42878322-42878331
45	MAZ	chr12:42875835-42878737	IMR90	lung:	n/a	n/a
46	POU2F2	chr12:42877900-42878351	GM12878	blood:	n/a	chr12:42878126-42878133 chr12:42878300-42878310 chr12:42878296-42878314 chr12:42878297-42878312 chr12:42878300-42878311 chr12:42878301-42878309 chr12:42878298-42878310 chr12:42878298-42878311
47	TCF7L2	chr12:42877380-42878957	HEK293	kidney:	n/a	n/a
48	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
49	JUND	chr12:42877887-42878806	H1-hESC	embryonic stem cell:	n/a	chr12:42878077-42878086
50	RAD21	chr12:42877777-42878449	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1626507	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669919	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669920	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2600937	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768431	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:115 , 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	chr12:42876000-42878400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:42876000-42878400	Active TSS	Colon Smooth Muscle	Colon
11	chr12:42876000-42878400	Active TSS	Rectal Smooth Muscle	rectum
12	chr12:42876000-42878600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:42876000-42878600	Active TSS	Aorta	Aorta
14	chr12:42876200-42878400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:42876200-42878400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:42876200-42878400	Active TSS	Fetal Kidney	kidney
17	chr12:42876200-42878400	Active TSS	Left Ventricle	heart
18	chr12:42876200-42878600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:42876400-42878400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:42876400-42878400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:42876400-42878400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:42876400-42878400	Active TSS	Osteobl	bone
23	chr12:42876400-42878600	Active TSS	Fetal Muscle Trunk	muscle
24	chr12:42876400-42878600	Active TSS	Psoas Muscle	Psoas
25	chr12:42876400-42878800	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:42876600-42878400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:42876600-42878400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr12:42876600-42878400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr12:42876600-42878400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
30	chr12:42876600-42878400	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:42876600-42878400	Active TSS	Stomach Mucosa	stomach
32	chr12:42876600-42878600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:42876600-42878600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:42876600-42878600	Active TSS	Fetal Brain Female	brain
35	chr12:42876600-42878600	Active TSS	Fetal Intestine Large	intestine
36	chr12:42876800-42878400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:42876800-42878400	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:42876800-42878400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:42876800-42878400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
40	chr12:42876800-42878400	Active TSS	Hela-S3	cervix
41	chr12:42877000-42878400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr12:42877000-42878400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:42877200-42878400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
44	chr12:42877200-42878400	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:42877200-42878400	Active TSS	Pancreas	Pancrea
46	chr12:42877200-42878600	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr12:42877200-42878600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:42877200-42878800	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:42877400-42878400	Bivalent/Poised TSS	Thymus	Thymus
50	chr12:42877600-42878400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood

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