Variant report

Variant	rs1491945
Chromosome Location	chr12:40618412-40618413
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	YY1	chr12:40618265-40618690	ECC-1	luminal epithelium:	n/a	chr12:40618496-40618505 chr12:40618618-40618627 chr12:40618491-40618505 chr12:40618406-40618420
2	MAZ	chr12:40617778-40619458	IMR90	lung:	n/a	chr12:40618784-40618793
3	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
4	MYC	chr12:40618386-40618427	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:40618394-40619008	U87	brain:	n/a	n/a
6	MAFK	chr12:40618336-40618648	IMR90	lung:	n/a	chr12:40618463-40618472 chr12:40618463-40618473
7	POLR2A	chr12:40618400-40619177	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:40618261-40619101	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr12:40617796-40619536	MCF10A-Er-Src	breast:	n/a	n/a
10	YY1	chr12:40618258-40619060	A549	lung:	n/a	chr12:40618853-40618867 chr12:40618496-40618505 chr12:40618618-40618627 chr12:40618806-40618820 chr12:40618491-40618505 chr12:40618406-40618420
11	E2F6	chr12:40618311-40619198	H1-hESC	embryonic stem cell:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
12	CHD2	chr12:40618371-40618897	Hela-S3	cervix:	n/a	chr12:40618748-40618758
13	TAF1	chr12:40618360-40618771	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr12:40618379-40619285	ECC-1	luminal epithelium:	n/a	chr12:40618784-40618793
15	E2F6	chr12:40618219-40619269	H1-hESC	embryonic stem cell:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
16	ZNF263	chr12:40617969-40619401	HEK293-T-REx	kidney:	n/a	chr12:40618700-40618709 chr12:40619158-40619167 chr12:40618762-40618771
17	HMGN3	chr12:40618383-40618877	K562	blood:	n/a	chr12:40618463-40618472
18	CHD2	chr12:40618363-40618575	HepG2	liver:	n/a	n/a
19	TAF1	chr12:40618228-40619031	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr12:40618215-40619232	ECC-1	luminal epithelium:	n/a	chr12:40618784-40618793
21	E2F6	chr12:40618259-40619239	A549	lung:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
22	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F6	chr12:40618398-40618534	K562	blood:	n/a	chr12:40618496-40618505
24	RELA	chr12:40617863-40619486	GM18951	blood:	n/a	n/a
25	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
26	POLR2A	chr12:40618322-40619091	NB4	blood:	n/a	n/a
27	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
28	POLR2A	chr12:40618391-40618413	MCF-7	breast:	n/a	n/a
29	POLR2A	chr12:40618176-40618906	PFSK-1	brain:	n/a	n/a
30	TCF12	chr12:40617809-40619771	A549	lung:	n/a	chr12:40618605-40618615
31	POLR2A	chr12:40618185-40619094	ECC-1	luminal epithelium:	n/a	n/a
32	REST	chr12:40618351-40619176	HL-60	blood:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
33	TCF12	chr12:40618263-40619269	ECC-1	luminal epithelium:	n/a	chr12:40618605-40618615
34	REST	chr12:40618023-40619814	A549	lung:	n/a	chr12:40618846-40618856 chr12:40618853-40618866 chr12:40618751-40618761
35	E2F6	chr12:40618338-40619118	A549	lung:	n/a	chr12:40618496-40618505 chr12:40618788-40618803 chr12:40618859-40618869
36	POLR2A	chr12:40618309-40619102	HL-60	blood:	n/a	n/a
37	POLR2A	chr12:40618200-40618896	IMR90	lung:	n/a	n/a
38	CHD2	chr12:40618314-40619207	GM12878	blood:	n/a	chr12:40618748-40618758
39	CREB1	chr12:40618240-40619019	A549	lung:	n/a	n/a
40	POLR2A	chr12:40618303-40618964	A549	lung:	n/a	n/a
41	POLR2A	chr12:40618340-40618790	K562	blood:	n/a	n/a
42	EP300	chr12:40618206-40619187	ECC-1	luminal epithelium:	n/a	n/a
43	ZBTB7A	chr12:40618206-40619074	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr12:40618300-40618450	SK-N-SH_RA	brain:	n/a	n/a
45	POLR2A	chr12:40618157-40619089	PFSK-1	brain:	n/a	n/a
46	CTCF	chr12:40618380-40618530	HCM	heart:	n/a	n/a
47	POLR2A	chr12:40618404-40618731	MCF-7	breast:	n/a	n/a
48	FOXA1	chr12:40618321-40618529	T-47D	breast:	n/a	n/a
49	JUND	chr12:40618137-40619013	A549	lung:	n/a	chr12:40618746-40618755 chr12:40618464-40618474
50	GATA3	chr12:40618121-40619606	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62622983..62623761-chr12:40618210..40619016,2	NB4	blood:

Variant related genes	Relation type
LRRK2	TF binding region
ENSG00000225342	TF binding region
ENSG00000255717	Chromatin interaction
ENSG00000168003	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10506143	0.82[AMR][1000 genomes]
rs10506146	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10506147	0.90[AMR][1000 genomes]
rs11175593	0.90[AMR][1000 genomes]
rs11564107	0.94[AMR][1000 genomes]
rs11564108	0.82[AMR][1000 genomes]
rs11564117	0.88[AMR][1000 genomes]
rs11564131	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11564153	0.82[AMR][1000 genomes]
rs11564187	0.82[AMR][1000 genomes]
rs11564190	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11564210	0.82[AMR][1000 genomes]
rs11564212	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11564214	0.83[AMR][1000 genomes]
rs11564218	0.82[AMR][1000 genomes]
rs12422544	0.81[AMR][1000 genomes]
rs12423419	0.85[AMR][1000 genomes]
rs12423551	0.84[AMR][1000 genomes]
rs12424294	0.82[AMR][1000 genomes]
rs12425561	0.90[AMR][1000 genomes]
rs12426643	0.90[AMR][1000 genomes]
rs12427022	0.82[AMR][1000 genomes]
rs1388597	0.94[AMR][1000 genomes]
rs17458808	0.84[AMR][1000 genomes]
rs17461387	0.90[AMR][1000 genomes]
rs17461575	0.90[AMR][1000 genomes]
rs17461692	0.84[AMR][1000 genomes]
rs17465610	0.90[AMR][1000 genomes]
rs17483919	0.90[AMR][1000 genomes]
rs17484003	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17484141	0.90[AMR][1000 genomes]
rs2131081	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28365206	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34567498	0.85[AMR][1000 genomes]
rs4767962	0.90[AMR][1000 genomes]
rs4767964	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4767965	0.90[AMR][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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40619200	Active TSS	Monocytes-CD14+_RO01746	blood
2	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
3	chr12:40616600-40619000	Active TSS	Primary B cells from peripheral blood	blood
4	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:40616800-40618800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
8	chr12:40617400-40619000	Active TSS	Duodenum Mucosa	Duodenum
9	chr12:40617400-40619200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:40617400-40619400	Active TSS	Small Intestine	intestine
11	chr12:40617400-40619600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
13	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
14	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:40617400-40621000	Active TSS	Right Atrium	heart
18	chr12:40617400-40621400	Active TSS	Aorta	Aorta
19	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:40617600-40620200	Active TSS	Ovary	ovary
21	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
23	chr12:40617800-40619000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:40617800-40619000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:40617800-40619000	Active TSS	Fetal Muscle Leg	muscle
26	chr12:40617800-40619200	Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr12:40617800-40619400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr12:40617800-40619400	Active TSS	NHLF	lung
29	chr12:40617800-40619600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr12:40617800-40619600	Active TSS	Right Ventricle	heart
31	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
33	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
34	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
35	chr12:40618000-40618600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr12:40618000-40618600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:40618000-40618800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:40618000-40618800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:40618000-40618800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:40618000-40618800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:40618000-40618800	Active TSS	HSMMtube	muscle
42	chr12:40618000-40619000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:40618000-40619000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr12:40618000-40619000	Active TSS	Primary T cells from cord blood	blood
45	chr12:40618000-40619000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:40618000-40619000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:40618000-40619000	Active TSS	Placenta	Placenta
48	chr12:40618000-40619200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr12:40618000-40619200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr12:40618000-40619200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links