Variant report

Variant	rs17490620
Chromosome Location	chr12:40620397-40620398
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	SP1	chr12:40619962-40620942	A549	lung:	n/a	n/a
2	BCL3	chr12:40620020-40620397	GM12878	blood:	n/a	chr12:40620179-40620188
3	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
4	FOS	chr12:40620387-40620755	HUVEC	blood vessel:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590 chr12:40620579-40620590
5	RCOR1	chr12:40619571-40620834	GM12878	blood:	n/a	n/a
6	FOXM1	chr12:40619959-40620444	GM12878	blood:	n/a	n/a
7	EP300	chr12:40619754-40620414	GM12878	blood:	n/a	n/a
8	SP1	chr12:40619931-40620415	GM12878	blood:	n/a	n/a
9	STAT3	chr12:40620389-40620778	MCF10A-Er-Src	breast:	n/a	chr12:40620581-40620590
10	MEF2C	chr12:40619898-40620535	GM12878	blood:	n/a	chr12:40620070-40620085
11	FOSL2	chr12:40620371-40620783	A549	lung:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590
12	POLR2A	chr12:40620137-40621088	PFSK-1	brain:	n/a	n/a
13	NFIC	chr12:40619893-40620538	GM12878	blood:	n/a	n/a
14	BHLHE40	chr12:40619850-40620471	GM12878	blood:	n/a	n/a
15	PAX5	chr12:40619914-40620505	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
16	EBF1	chr12:40619613-40620945	GM12878	blood:	n/a	chr12:40620810-40620819
17	FOS	chr12:40620393-40620808	MCF10A-Er-Src	breast:	n/a	chr12:40620464-40620476 chr12:40620581-40620590 chr12:40620580-40620590 chr12:40620580-40620590 chr12:40620579-40620590
18	CHD2	chr12:40619992-40620786	GM12878	blood:	n/a	n/a
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	SPI1	chr12:40619630-40620808	GM12878	blood:	n/a	chr12:40620179-40620188
27	IRF4	chr12:40619955-40620454	GM12878	blood:	n/a	n/a
28	GATA3	chr12:40620250-40620578	SH-SY5Y	brain:	n/a	n/a
29	TBL1XR1	chr12:40619800-40620456	GM12878	blood:	n/a	n/a
30	MTA3	chr12:40619871-40620464	GM12878	blood:	n/a	n/a
31	EP300	chr12:40619571-40620612	GM12878	blood:	n/a	chr12:40620580-40620589
32	REST	chr12:40619923-40620965	A549	lung:	n/a	n/a
33	BCLAF1	chr12:40620014-40620432	GM12878	blood:	n/a	chr12:40620179-40620188
34	BATF	chr12:40619951-40620402	GM12878	blood:	n/a	chr12:40620016-40620024
35	ATF2	chr12:40619916-40620447	GM12878	blood:	n/a	n/a
36	TAF1	chr12:40620125-40620863	PFSK-1	brain:	n/a	n/a
37	POU2F2	chr12:40619965-40620439	GM12878	blood:	n/a	chr12:40620095-40620106
38	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
39	CUX1	chr12:40619785-40620484	GM12878	blood:	n/a	n/a
40	RUNX3	chr12:40619856-40620514	GM12878	blood:	n/a	n/a
41	BCLAF1	chr12:40619904-40620434	GM12878	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
42	CREB1	chr12:40620379-40620792	A549	lung:	n/a	n/a
43	MAX	chr12:40620102-40620829	A549	lung:	n/a	n/a
44	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
45	ATF2	chr12:40619878-40620536	GM12878	blood:	n/a	n/a
46	PAX5	chr12:40619991-40620439	GM12891	blood:	n/a	chr12:40620012-40620021 chr12:40620179-40620188
47	GATA2	chr12:40620109-40620840	HUVEC	blood vessel:	n/a	chr12:40620785-40620792 chr12:40620781-40620794 chr12:40620774-40620791
48	TCF12	chr12:40619934-40620982	A549	lung:	n/a	n/a
49	SPI1	chr12:40619901-40620432	GM12891	blood:	n/a	chr12:40620179-40620188
50	MXI1	chr12:40619871-40620851	GM12878	blood:	n/a	n/a

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: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11564113	1.00[JPT][hapmap]
rs11613829	1.00[JPT][hapmap]
rs17442095	1.00[JPT][hapmap]
rs17442346	1.00[JPT][hapmap]
rs17442353	1.00[JPT][hapmap]
rs17442490	1.00[JPT][hapmap]
rs17442882	1.00[JPT][hapmap]
rs17443421	1.00[JPT][hapmap]
rs17443552	1.00[JPT][hapmap]
rs17444103	1.00[JPT][hapmap]
rs17444542	1.00[JPT][hapmap]
rs17458257	1.00[JPT][hapmap]
rs17458745	1.00[JPT][hapmap]
rs17458773	1.00[JPT][hapmap]
rs17458974	1.00[JPT][hapmap]
rs17460894	1.00[JPT][hapmap]
rs17460992	1.00[JPT][hapmap]
rs17465716	1.00[JPT][hapmap]
rs17465849	1.00[JPT][hapmap]
rs17465891	1.00[JPT][hapmap]
rs17466030	1.00[JPT][hapmap]
rs17466220	1.00[JPT][hapmap]
rs17466269	1.00[JPT][hapmap]
rs17466297	1.00[JPT][hapmap]
rs17466339	1.00[JPT][hapmap]
rs17466451	1.00[JPT][hapmap]
rs17466633	1.00[JPT][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489225	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17489302	1.00[AMR][1000 genomes]
rs17489379	1.00[AMR][1000 genomes]
rs17489459	1.00[JPT][hapmap]
rs17489480	1.00[JPT][hapmap]
rs17489666	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17489715	1.00[AMR][1000 genomes]
rs17489722	1.00[AMR][1000 genomes]
rs17489889	1.00[AMR][1000 genomes]
rs17490013	1.00[JPT][hapmap]
rs17490418	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17490578	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17490585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17490599	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17490762	1.00[JPT][hapmap]
rs17491110	1.00[JPT][hapmap]
rs17491410	1.00[JPT][hapmap]
rs17492138	1.00[JPT][hapmap]
rs17518014	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17518050	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518071	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518183	1.00[JPT][hapmap]
rs17518204	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518253	1.00[AMR][1000 genomes]
rs17518273	1.00[AMR][1000 genomes]
rs17518364	1.00[AMR][1000 genomes]
rs17518427	1.00[JPT][hapmap]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
rs17518770	1.00[AMR][1000 genomes]
rs17518805	1.00[AMR][1000 genomes]
rs17518992	1.00[AMR][1000 genomes]
rs17519566	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17519797	1.00[JPT][hapmap]
rs17520634	1.00[JPT][hapmap]
rs17520655	1.00[JPT][hapmap]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
rs28365202	1.00[JPT][hapmap]
rs28365243	1.00[JPT][hapmap]
rs28370776	1.00[AMR][1000 genomes]
rs28370777	1.00[AMR][1000 genomes]
rs28370778	1.00[AMR][1000 genomes]
rs28370780	1.00[AMR][1000 genomes]
rs28370783	1.00[AMR][1000 genomes]
rs28370786	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370792	1.00[JPT][hapmap]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[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:65 , 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	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
12	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
13	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
14	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
16	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
17	chr12:40618000-40620800	Active TSS	Lung	lung
18	chr12:40618000-40621000	Active TSS	A549	lung
19	chr12:40618200-40620600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr12:40618200-40620800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr12:40618200-40620800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr12:40618800-40620800	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:40618800-40621200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr12:40619000-40621000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:40619000-40621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr12:40619200-40621200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr12:40619400-40620400	Weak transcription	Hela-S3	cervix
28	chr12:40619400-40620800	Active TSS	Brain Cingulate Gyrus	brain
29	chr12:40619400-40620800	Active TSS	Duodenum Mucosa	Duodenum
30	chr12:40619400-40621000	Enhancers	HUVEC	blood vessel
31	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
32	chr12:40619400-40644400	Weak transcription	Gastric	stomach
33	chr12:40619600-40620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:40619600-40620600	Weak transcription	Esophagus	oesophagus
35	chr12:40619600-40620600	Weak transcription	Left Ventricle	heart
36	chr12:40619600-40620600	Weak transcription	Pancreas	Pancrea
37	chr12:40619600-40621000	Enhancers	HMEC	breast
38	chr12:40619600-40621000	Enhancers	NHEK	skin
39	chr12:40619600-40621000	Enhancers	Osteobl	bone
40	chr12:40619600-40636400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
43	chr12:40619800-40620400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr12:40619800-40620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:40620000-40620400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr12:40620000-40620400	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr12:40620000-40620600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:40620000-40620600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:40620000-40621000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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