Variant report

Variant	rs11541137
Chromosome Location	chr2:128145771-128145772
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	POLR2A	chr2:128144758-128146110	MCF-7	breast:	n/a	n/a
2	MAX	chr2:128144457-128146041	HepG2	liver:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
3	POLR2A	chr2:128145745-128145977	H1-hESC	embryonic stem cell:	n/a	n/a
4	RUNX3	chr2:128144347-128146478	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:128144343-128146428	GM12891	blood:	n/a	n/a
6	EP300	chr2:128144468-128146129	HepG2	liver:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
7	ELF1	chr2:128145289-128145990	HepG2	liver:	n/a	chr2:128145438-128145447
8	POLR2A	chr2:128144624-128146116	MCF-7	breast:	n/a	n/a
9	MAX	chr2:128144669-128146230	Hela-S3	cervix:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
10	POLR2A	chr2:128145266-128146056	SK-N-SH	brain:	n/a	n/a
11	SIN3A	chr2:128144430-128146062	H1-hESC	embryonic stem cell:	n/a	chr2:128145470-128145481 chr2:128144859-128144870 chr2:128145893-128145902
12	RELA	chr2:128145433-128146520	GM10847	blood:	n/a	n/a
13	POLR2A	chr2:128144844-128146037	K562	blood:	n/a	n/a
14	POLR2A	chr2:128144934-128146008	K562	blood:	n/a	n/a
15	STAT5A	chr2:128145671-128146372	GM12878	blood:	n/a	n/a
16	MAX	chr2:128145370-128146614	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
17	MAX	chr2:128144496-128146255	GM12878	blood:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
18	CHD1	chr2:128143649-128147067	IMR90	lung:	n/a	chr2:128145167-128145177
19	POLR2A	chr2:128144643-128146053	Gliobla	brain:	n/a	n/a
20	REST	chr2:128145625-128146354	A549	lung:	n/a	chr2:128145906-128145915
21	POLR2A	chr2:128145699-128146462	GM12891	blood:	n/a	n/a
22	SIN3AK20	chr2:128145647-128146072	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr2:128144909-128146132	Hela-S3	cervix:	n/a	n/a
24	REST	chr2:128145270-128146022	HepG2	liver:	n/a	chr2:128145442-128145455 chr2:128145906-128145915
25	EBF1	chr2:128145427-128145933	GM12878	blood:	n/a	n/a
26	NRF1	chr2:128144336-128146260	SK-N-SH	brain:	n/a	chr2:128145663-128145674 chr2:128145663-128145677 chr2:128145665-128145674 chr2:128145628-128145639 chr2:128145660-128145674 chr2:128145663-128145674
27	EGR1	chr2:128145443-128145916	H1-hESC	embryonic stem cell:	n/a	chr2:128145683-128145698 chr2:128145683-128145697 chr2:128145685-128145695 chr2:128145664-128145673 chr2:128145685-128145695 chr2:128145685-128145696 chr2:128145699-128145713 chr2:128145681-128145695 chr2:128145684-128145697
28	POLR2A	chr2:128144307-128146229	SK-N-MC	brain:	n/a	n/a
29	EGR1	chr2:128144704-128146189	HCT-116	colon:	n/a	chr2:128145683-128145698 chr2:128145683-128145697 chr2:128145685-128145695 chr2:128145664-128145673 chr2:128145685-128145695 chr2:128145685-128145696 chr2:128145699-128145713 chr2:128145681-128145695 chr2:128145684-128145697 chr2:128145069-128145083
30	HMGN3	chr2:128144751-128146078	K562	blood:	n/a	n/a
31	HEY1	chr2:128145679-128146157	HepG2	liver:	n/a	n/a
32	ATF2	chr2:128145303-128146473	GM12878	blood:	n/a	chr2:128145544-128145558 chr2:128145565-128145579
33	IRF1	chr2:128145473-128146007	K562	blood:	n/a	chr2:128145679-128145693
34	ELF1	chr2:128144693-128145994	GM12878	blood:	n/a	chr2:128145438-128145447 chr2:128145117-128145129
35	MAX	chr2:128145697-128146059	SK-N-SH	brain:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
36	FOXM1	chr2:128144675-128146196	GM12878	blood:	n/a	n/a
37	EGR1	chr2:128145523-128145856	GM12878	blood:	n/a	chr2:128145683-128145698 chr2:128145683-128145697 chr2:128145685-128145695 chr2:128145664-128145673 chr2:128145685-128145695 chr2:128145685-128145696 chr2:128145699-128145713 chr2:128145681-128145695 chr2:128145684-128145697
38	NRF1	chr2:128145424-128146292	GM12878	blood:	n/a	chr2:128145663-128145674 chr2:128145663-128145677 chr2:128145665-128145674 chr2:128145628-128145639 chr2:128145660-128145674 chr2:128145663-128145674
39	EP300	chr2:128144748-128146508	GM12878	blood:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
40	CEBPD	chr2:128144736-128145994	HepG2	liver:	n/a	n/a
41	RELA	chr2:128145378-128146483	GM19099	blood:	n/a	n/a
42	TFAP2A	chr2:128144693-128146275	Hela-S3	cervix:	n/a	chr2:128145602-128145617 chr2:128145773-128145788
43	POLR2A	chr2:128144696-128146001	HepG2	liver:	n/a	n/a
44	RAD21	chr2:128144600-128146451	IMR90	lung:	n/a	chr2:128144843-128144853
45	POLR2A	chr2:128144667-128146031	GM12878	blood:	n/a	n/a
46	MYBL2	chr2:128144475-128146159	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:128145181-128146137	GM12892	blood:	n/a	n/a
48	POLR2A	chr2:128144849-128146088	H1-hESC	embryonic stem cell:	n/a	n/a
49	MBD4	chr2:128145684-128146544	HepG2	liver:	n/a	n/a
50	MAX	chr2:128144503-128146173	ECC-1	luminal epithelium:	n/a	chr2:128145890-128145905 chr2:128145892-128145902

No.	Distal block	Cell Line	Cell type
1	chr2:128143986..128147167-chr2:128178825..128181533,4	MCF-7	breast:
2	chr2:120435826..120437483-chr2:128143933..128146415,2	MCF-7	breast:
3	chr17:45726968..45727634-chr2:128145066..128146033,2	HCT-116	colon:
4	chr13:21347604..21348144-chr2:128145436..128146340,2	NB4	blood:
5	chr2:128100404..128103030-chr2:128144500..128146639,3	MCF-7	breast:
6	chr2:128143823..128146469-chr2:128456940..128459025,2	MCF-7	breast:
7	chr1:23885549..23886356-chr2:128145254..128145774,2	HCT-116	colon:
8	chr2:128050445..128053038-chr2:128144842..128147674,3	K562	blood:
9	chr2:128145128..128146772-chr2:128281228..128284838,3	MCF-7	breast:
10	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROC-1	chr2:128145685-128145887	NONHSAT074148

Variant related genes	Relation type
MAP3K2	TF binding region
ENSG00000236682	TF binding region
ENSG00000173349	Chromatin interaction
ENSG00000144120	Chromatin interaction
ENSG00000169967	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000150456	Chromatin interaction
ENSG00000115718	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000264075	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000117318	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1011019	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10209483	0.82[EUR][1000 genomes]
rs10496661	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10850	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11679414	0.84[EUR][1000 genomes]
rs11680877	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11680949	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11691088	0.83[EUR][1000 genomes]
rs11691916	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11692990	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2896979	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3958415	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4150402	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4150404	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4150471	0.83[AFR][1000 genomes]
rs4150476	0.83[AFR][1000 genomes]
rs4662719	0.83[AFR][1000 genomes]
rs4662720	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59378658	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61422716	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72845975	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72845976	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72845991	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72845993	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72845997	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72846002	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72848604	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72848615	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72848616	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72848618	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7556675	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7562428	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7607907	0.92[AMR][1000 genomes];0.95[EUR][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	esv3346398	chr2:128143907-128146455	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3327412	chr2:128144082-128146880	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11541137	ERCC3	cis	Nerve Tibial	GTEx
rs11541137	ERCC3	cis	Esophagus Muscularis	GTEx
rs11541137	ERCC3	cis	Adipose Subcutaneous	GTEx
rs11541137	ERCC3	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128143200-128146200	Active TSS	Psoas Muscle	Psoas
2	chr2:128143400-128145800	Active TSS	Muscle Satellite Cultured Cells	--
3	chr2:128143400-128145800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:128143600-128145800	Active TSS	Fetal Intestine Large	intestine
5	chr2:128143600-128145800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr2:128143600-128146000	Active TSS	HSMMtube	muscle
7	chr2:128143800-128145800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:128143800-128145800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:128143800-128145800	Active TSS	Duodenum Mucosa	Duodenum
10	chr2:128143800-128145800	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr2:128143800-128146000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:128143800-128146000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:128143800-128146000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:128143800-128146000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:128143800-128146000	Active TSS	A549	lung
16	chr2:128143800-128146000	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:128143800-128146000	Active TSS	NHLF	lung
18	chr2:128143800-128146200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:128143800-128146200	Active TSS	Right Atrium	heart
20	chr2:128144000-128145800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:128144000-128145800	Active TSS	Thymus	Thymus
22	chr2:128144000-128145800	Active TSS	Hela-S3	cervix
23	chr2:128144000-128145800	Active TSS	HSMM	muscle
24	chr2:128144000-128146000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:128144000-128146000	Active TSS	Brain Angular Gyrus	brain
26	chr2:128144000-128146000	Active TSS	Brain Cingulate Gyrus	brain
27	chr2:128144000-128146000	Active TSS	Brain Hippocampus Middle	brain
28	chr2:128144000-128146000	Active TSS	Ovary	ovary
29	chr2:128144000-128146000	Active TSS	Stomach Smooth Muscle	stomach
30	chr2:128144000-128146200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:128144000-128146200	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr2:128144000-128146200	Active TSS	Right Ventricle	heart
33	chr2:128144200-128145800	Active TSS	HMEC	breast
34	chr2:128144200-128146000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr2:128144200-128146000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:128144200-128146000	Active TSS	K562	blood
37	chr2:128144200-128146200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr2:128144200-128146200	Active TSS	Fetal Brain Female	brain
39	chr2:128144200-128146200	Active TSS	GM12878-XiMat	blood
40	chr2:128144200-128146200	Active TSS	NHDF-Ad	bronchial
41	chr2:128144200-128146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:128144200-128146600	Active TSS	Colonic Mucosa	Colon
43	chr2:128144400-128145800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:128144400-128145800	Active TSS	Stomach Mucosa	stomach
45	chr2:128144400-128146000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr2:128144400-128146000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr2:128144400-128146000	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr2:128144400-128146000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr2:128144400-128146000	Active TSS	Placenta	Placenta
50	chr2:128144400-128146000	Active TSS	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links