Variant report

Variant	rs17465744
Chromosome Location	chr12:40620007-40620008
allele	C/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	SP1	chr12:40619962-40620942	A549	lung:	n/a	n/a
2	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
3	RCOR1	chr12:40619571-40620834	GM12878	blood:	n/a	n/a
4	FOXM1	chr12:40619959-40620444	GM12878	blood:	n/a	n/a
5	EP300	chr12:40619754-40620414	GM12878	blood:	n/a	n/a
6	SP1	chr12:40619931-40620415	GM12878	blood:	n/a	n/a
7	BCL11A	chr12:40619935-40620396	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
8	MEF2C	chr12:40619898-40620535	GM12878	blood:	n/a	chr12:40620070-40620085
9	NFIC	chr12:40619893-40620538	GM12878	blood:	n/a	n/a
10	BHLHE40	chr12:40619850-40620471	GM12878	blood:	n/a	n/a
11	PAX5	chr12:40619914-40620505	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
12	EBF1	chr12:40619613-40620945	GM12878	blood:	n/a	chr12:40620810-40620819
13	BCL11A	chr12:40619996-40620353	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
14	ZNF384	chr12:40619736-40620307	GM12878	blood:	n/a	n/a
15	BATF	chr12:40619967-40620344	GM12878	blood:	n/a	chr12:40620016-40620024
16	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
17	CHD2	chr12:40619992-40620786	GM12878	blood:	n/a	n/a
18	SPI1	chr12:40619900-40620377	GM12878	blood:	n/a	chr12:40620179-40620188
19	RELA	chr12:40619964-40621083	GM19099	blood:	n/a	n/a
20	RUNX3	chr12:40619962-40620455	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
22	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
23	MEF2A	chr12:40619951-40620468	GM12878	blood:	n/a	chr12:40620070-40620085
24	MEF2A	chr12:40619876-40620526	GM12878	blood:	n/a	chr12:40620070-40620085
25	TBP	chr12:40619440-40620658	GM12878	blood:	n/a	n/a
26	EP300	chr12:40619898-40620352	GM12878	blood:	n/a	n/a
27	SPI1	chr12:40619630-40620808	GM12878	blood:	n/a	chr12:40620179-40620188
28	IRF4	chr12:40619955-40620454	GM12878	blood:	n/a	n/a
29	IRF4	chr12:40619948-40620365	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr12:40619800-40620456	GM12878	blood:	n/a	n/a
31	MTA3	chr12:40619871-40620464	GM12878	blood:	n/a	n/a
32	EP300	chr12:40619571-40620612	GM12878	blood:	n/a	chr12:40620580-40620589
33	REST	chr12:40619923-40620965	A549	lung:	n/a	n/a
34	BATF	chr12:40619951-40620402	GM12878	blood:	n/a	chr12:40620016-40620024
35	ATF2	chr12:40619916-40620447	GM12878	blood:	n/a	n/a
36	POU2F2	chr12:40619965-40620439	GM12878	blood:	n/a	chr12:40620095-40620106
37	FOSL2	chr12:40619929-40620993	A549	lung:	n/a	chr12:40620149-40620158 chr12:40620464-40620476 chr12:40620212-40620219 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590
38	CUX1	chr12:40619785-40620484	GM12878	blood:	n/a	n/a
39	RUNX3	chr12:40619856-40620514	GM12878	blood:	n/a	n/a
40	BCLAF1	chr12:40619904-40620434	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
41	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
42	ATF2	chr12:40619878-40620536	GM12878	blood:	n/a	n/a
43	PAX5	chr12:40619991-40620439	GM12891	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
44	TCF12	chr12:40619934-40620982	A549	lung:	n/a	n/a
45	SPI1	chr12:40619901-40620432	GM12891	blood:	n/a	chr12:40620179-40620188
46	MXI1	chr12:40619871-40620851	GM12878	blood:	n/a	n/a
47	NFIC	chr12:40619760-40620678	GM12878	blood:	n/a	n/a
48	SP1	chr12:40619921-40620847	A549	lung:	n/a	n/a
49	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
50	PAX5	chr12:40620007-40620390	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
ENSG00000225342	TF binding region
ENSG00000225342	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17443387	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17444152	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17465737	1.00[CEU][hapmap]

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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
2	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
5	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:40617400-40621000	Active TSS	Right Atrium	heart
10	chr12:40617400-40621400	Active TSS	Aorta	Aorta
11	chr12:40617600-40620200	Active TSS	Ovary	ovary
12	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
14	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
15	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
16	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
17	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
18	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
19	chr12:40618000-40620800	Active TSS	Lung	lung
20	chr12:40618000-40621000	Active TSS	A549	lung
21	chr12:40618200-40620600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr12:40618200-40620800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:40618200-40620800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr12:40618800-40620800	Flanking Active TSS	GM12878-XiMat	blood
25	chr12:40618800-40621200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr12:40619000-40621000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:40619000-40621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:40619200-40620200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:40619200-40620200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr12:40619200-40620200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:40619200-40621200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr12:40619400-40620200	Active TSS	Placenta	Placenta
33	chr12:40619400-40620200	Weak transcription	NH-A	brain
34	chr12:40619400-40620400	Weak transcription	Hela-S3	cervix
35	chr12:40619400-40620800	Active TSS	Brain Cingulate Gyrus	brain
36	chr12:40619400-40620800	Active TSS	Duodenum Mucosa	Duodenum
37	chr12:40619400-40621000	Enhancers	HUVEC	blood vessel
38	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
39	chr12:40619400-40644400	Weak transcription	Gastric	stomach
40	chr12:40619600-40620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:40619600-40620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:40619600-40620600	Weak transcription	Esophagus	oesophagus
43	chr12:40619600-40620600	Weak transcription	Left Ventricle	heart
44	chr12:40619600-40620600	Weak transcription	Pancreas	Pancrea
45	chr12:40619600-40621000	Enhancers	HMEC	breast
46	chr12:40619600-40621000	Enhancers	NHEK	skin
47	chr12:40619600-40621000	Enhancers	Osteobl	bone
48	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart

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