Variant report

Variant	rs740059
Chromosome Location	chr12:4671490-4671491
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	UBTF	chr12:4671177-4671657	K562	blood:	n/a	n/a
2	ZNF263	chr12:4671152-4671667	HEK293-T-REx	kidney:	n/a	chr12:4671331-4671340
3	MAX	chr12:4670951-4672043	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:4671282-4671528	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr12:4671274-4671586	K562	blood:	n/a	n/a
6	CHD2	chr12:4671155-4671735	H1-hESC	embryonic stem cell:	n/a	chr12:4671418-4671428 chr12:4671308-4671318
7	POLR2A	chr12:4671016-4672075	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:4671264-4671571	K562	blood:	n/a	n/a
9	CCNT2	chr12:4671231-4671538	K562	blood:	n/a	n/a
10	POLR2A	chr12:4671206-4671583	K562	blood:	n/a	n/a
11	CTCF	chr12:4671340-4671490	SK-N-SH_RA	brain:	n/a	chr12:4671384-4671397
12	UBTF	chr12:4671335-4671551	K562	blood:	n/a	n/a
13	POLR2A	chr12:4671115-4671622	ECC-1	luminal epithelium:	n/a	n/a
14	TEAD4	chr12:4671304-4671808	H1-hESC	embryonic stem cell:	n/a	n/a
15	SP4	chr12:4671223-4671613	H1-hESC	embryonic stem cell:	n/a	chr12:4671334-4671350
16	CTCF	chr12:4671480-4671630	NHDF-neo	bronchial:	n/a	n/a
17	TAF1	chr12:4671271-4671688	H1-hESC	embryonic stem cell:	n/a	n/a
18	NANOG	chr12:4671295-4671501	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr12:4671143-4671690	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:4671186-4671596	K562	blood:	n/a	n/a
21	USF2	chr12:4671358-4671700	H1-hESC	embryonic stem cell:	n/a	chr12:4671385-4671401 chr12:4671377-4671393 chr12:4671415-4671431
22	JUN	chr12:4671251-4671527	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTBP2	chr12:4671098-4671990	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:4671352-4671542	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr12:4671398-4671553	MCF-7	breast:	n/a	n/a
26	SIN3A	chr12:4671132-4671763	H1-hESC	embryonic stem cell:	n/a	chr12:4671356-4671367
27	MAX	chr12:4670873-4671753	K562	blood:	n/a	n/a
28	MXI1	chr12:4671175-4671541	HepG2	liver:	n/a	chr12:4671318-4671333 chr12:4671316-4671331
29	TBP	chr12:4671190-4671761	H1-hESC	embryonic stem cell:	n/a	n/a
30	TEAD4	chr12:4671266-4671597	K562	blood:	n/a	n/a
31	POLR2A	chr12:4671324-4671806	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:4670888-4671869	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr12:4671031-4671655	K562	blood:	n/a	n/a
34	E2F6	chr12:4671177-4671686	K562	blood:	n/a	chr12:4671419-4671431
35	SETDB1	chr12:4671015-4671677	U2OS	brain:	n/a	n/a
36	ZMIZ1	chr12:4671201-4671549	K562	blood:	n/a	n/a
37	MAX	chr12:4670905-4672117	H1-hESC	embryonic stem cell:	n/a	n/a
38	E2F6	chr12:4671280-4671493	K562	blood:	n/a	chr12:4671419-4671431
39	HCFC1	chr12:4671181-4671660	K562	blood:	n/a	n/a
40	POLR2A	chr12:4670878-4672143	K562	blood:	n/a	n/a
41	HMGN3	chr12:4671226-4671571	K562	blood:	n/a	n/a
42	MAZ	chr12:4670931-4672091	IMR90	lung:	n/a	n/a
43	POLR2A	chr12:4671098-4671753	U87	brain:	n/a	n/a
44	MAX	chr12:4671002-4671990	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:4671226-4671541	HUVEC	blood vessel:	n/a	n/a
46	MYC	chr12:4671096-4671640	K562	blood:	n/a	n/a
47	CEBPD	chr12:4671352-4671548	HepG2	liver:	n/a	n/a
48	CHD2	chr12:4671309-4671776	K562	blood:	n/a	chr12:4671418-4671428
49	YY1	chr12:4671268-4671539	K562	blood:	n/a	chr12:4671394-4671408
50	RCOR1	chr12:4671445-4671582	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4671422..4673318-chr12:4674512..4676464,2	K562	blood:
2	chr12:4671378..4673735-chr15:65588243..65590469,2	K562	blood:

Variant related genes	Relation type
DYRK4	TF binding region
ENSG00000199568	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1038332	chr12:4627992-4689300	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541362	chr12:4627992-4689300	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740059	PLEKHG6	cis	parietal	SCAN
rs740059	LAG3	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4652000-4671800	Strong transcription	Dnd41	blood
2	chr12:4658400-4671600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:4659000-4671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:4668400-4673800	Weak transcription	GM12878-XiMat	blood
5	chr12:4670200-4679600	Weak transcription	Hela-S3	cervix
6	chr12:4670400-4675200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:4670400-4679200	Weak transcription	A549	lung
8	chr12:4670800-4672200	Enhancers	Fetal Thymus	thymus
9	chr12:4671000-4671600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:4671000-4671600	Active TSS	Brain Anterior Caudate	brain
11	chr12:4671000-4671600	Active TSS	Colon Smooth Muscle	Colon
12	chr12:4671000-4671800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:4671000-4671800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:4671000-4671800	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr12:4671000-4671800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:4671000-4671800	Flanking Active TSS	K562	blood
17	chr12:4671000-4671800	Flanking Active TSS	NHLF	lung
18	chr12:4671000-4672000	Enhancers	Liver	Liver
19	chr12:4671000-4672000	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr12:4671000-4672000	Active TSS	Brain Substantia Nigra	brain
21	chr12:4671000-4672000	Bivalent Enhancer	Fetal Brain Male	brain
22	chr12:4671000-4672000	Enhancers	Stomach Mucosa	stomach
23	chr12:4671000-4672000	Enhancers	Spleen	Spleen
24	chr12:4671000-4672200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:4671200-4671600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:4671200-4671600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:4671200-4671600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:4671200-4671600	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr12:4671200-4671600	Active TSS	Primary T cells from cord blood	blood
30	chr12:4671200-4671600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:4671200-4671600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:4671200-4671600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:4671200-4671600	Active TSS	Ovary	ovary
34	chr12:4671200-4671600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
35	chr12:4671200-4671600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr12:4671200-4671600	Flanking Active TSS	Right Ventricle	heart
37	chr12:4671200-4671600	Active TSS	HepG2	liver
38	chr12:4671200-4671600	Flanking Active TSS	HSMM	muscle
39	chr12:4671200-4671800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:4671200-4671800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:4671200-4671800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:4671200-4671800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:4671200-4671800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:4671200-4671800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:4671200-4671800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:4671200-4671800	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr12:4671200-4671800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:4671200-4671800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr12:4671200-4671800	Active TSS	Fetal Brain Female	brain
50	chr12:4671200-4671800	Flanking Active TSS	Fetal Intestine Small	intestine

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