Variant report

Variant	rs11940090
Chromosome Location	chr4:166299853-166299854
allele	G/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	MAX	chr4:166299703-166300795	HCT-116	colon:	n/a	chr4:166300110-166300120
2	CTCF	chr4:166299833-166300516	A549	lung:	n/a	chr4:166300277-166300290
3	YY1	chr4:166299783-166300764	ECC-1	luminal epithelium:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300717-166300731 chr4:166300345-166300359 chr4:166300354-166300363
4	MAX	chr4:166299734-166300813	HepG2	liver:	n/a	chr4:166300110-166300120
5	BHLHE40	chr4:166299748-166300500	HepG2	liver:	n/a	chr4:166300345-166300361 chr4:166300276-166300292
6	POLR2A	chr4:166299820-166300645	HepG2	liver:	n/a	n/a
7	YY1	chr4:166299790-166300725	SK-N-SH_RA	brain:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300345-166300359 chr4:166300354-166300363
8	REST	chr4:166299004-166301874	H1-neurons	neurons:	n/a	chr4:166300166-166300179 chr4:166299047-166299055 chr4:166300164-166300182
9	MXI1	chr4:166299094-166301418	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr4:166299850-166300421	ECC-1	luminal epithelium:	n/a	n/a
11	REST	chr4:166299527-166300557	H1-neurons	neurons:	n/a	chr4:166300166-166300179 chr4:166300164-166300182
12	MAX	chr4:166299828-166300862	ECC-1	luminal epithelium:	n/a	chr4:166300110-166300120
13	YY1	chr4:166299822-166300807	H1-hESC	embryonic stem cell:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300717-166300731 chr4:166300345-166300359 chr4:166300354-166300363
14	POLR2A	chr4:166299620-166301519	H1-neurons	neurons:	n/a	n/a
15	MAX	chr4:166299790-166300902	HepG2	liver:	n/a	chr4:166300110-166300120
16	POLR2A	chr4:166299837-166300451	HepG2	liver:	n/a	n/a
17	RCOR1	chr4:166299808-166300421	HepG2	liver:	n/a	n/a
18	MYBL2	chr4:166299818-166300376	HepG2	liver:	n/a	n/a
19	HEY1	chr4:166299764-166300676	HepG2	liver:	n/a	chr4:166300352-166300367 chr4:166300349-166300364 chr4:166300357-166300372
20	CTCF	chr4:166299720-166299870	WI-38	lung:	n/a	n/a
21	EP300	chr4:166299789-166300663	HepG2	liver:	n/a	chr4:166299816-166299825 chr4:166300355-166300371 chr4:166300353-166300362 chr4:166300277-166300293 chr4:166300351-166300360
22	TAF1	chr4:166299636-166300679	H1-neurons	neurons:	n/a	n/a
23	CREB1	chr4:166299826-166300446	H1-hESC	embryonic stem cell:	n/a	n/a
24	CHD1	chr4:166299784-166300662	IMR90	lung:	n/a	n/a
25	EP300	chr4:166299661-166300527	ECC-1	luminal epithelium:	n/a	chr4:166299816-166299825 chr4:166300355-166300371 chr4:166300353-166300362 chr4:166300277-166300293 chr4:166300351-166300360
26	MAX	chr4:166299814-166300835	MCF-7	breast:	n/a	chr4:166300110-166300120
27	SRF	chr4:166299848-166300449	ECC-1	luminal epithelium:	n/a	chr4:166300307-166300317
28	MAX	chr4:166299667-166300765	ECC-1	luminal epithelium:	n/a	chr4:166300110-166300120
29	YY1	chr4:166299778-166300834	ECC-1	luminal epithelium:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300717-166300731 chr4:166300345-166300359 chr4:166300354-166300363
30	YY1	chr4:166299844-166300335	HepG2	liver:	n/a	chr4:166300286-166300300
31	YY1	chr4:166299804-166300359	SK-N-SH_RA	brain:	n/a	chr4:166300286-166300300 chr4:166300345-166300359
32	KAP1	chr4:166299779-166300585	HEK293	kidney:	n/a	n/a
33	TEAD4	chr4:166299768-166300460	ECC-1	luminal epithelium:	n/a	n/a
34	TCF12	chr4:166299826-166300541	ECC-1	luminal epithelium:	n/a	chr4:166300068-166300078
35	TAF1	chr4:166299658-166301299	H1-neurons	neurons:	n/a	n/a
36	MYBL2	chr4:166299762-166300455	HepG2	liver:	n/a	n/a
37	CREB1	chr4:166299714-166300419	HepG2	liver:	n/a	n/a
38	YY1	chr4:166299846-166300785	HepG2	liver:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300717-166300731 chr4:166300345-166300359 chr4:166300354-166300363
39	CTCF	chr4:166299677-166301321	SK-N-SH	brain:	n/a	chr4:166300937-166300945 chr4:166300277-166300290
40	TEAD4	chr4:166299625-166300431	ECC-1	luminal epithelium:	n/a	n/a
41	JUND	chr4:166299423-166300536	SK-N-SH	brain:	n/a	chr4:166299945-166299956
42	SIN3A	chr4:166299818-166300681	H1-hESC	embryonic stem cell:	n/a	chr4:166300136-166300149 chr4:166300358-166300369 chr4:166300279-166300290
43	JUND	chr4:166299805-166300302	H1-hESC	embryonic stem cell:	n/a	chr4:166299945-166299956
44	YY1	chr4:166299796-166301083	H1-hESC	embryonic stem cell:	n/a	chr4:166300355-166300366 chr4:166300286-166300300 chr4:166300717-166300731 chr4:166300345-166300359 chr4:166300354-166300363
45	MAX	chr4:166299617-166300816	HCT-116	colon:	n/a	chr4:166300110-166300120
46	POLR2A	chr4:166299602-166301387	H1-neurons	neurons:	n/a	n/a
47	FOXA1	chr4:166299838-166300274	HepG2	liver:	n/a	n/a
48	CREB1	chr4:166299827-166300403	H1-hESC	embryonic stem cell:	n/a	n/a
49	NFIC	chr4:166299720-166300329	ECC-1	luminal epithelium:	n/a	n/a
50	CREB1	chr4:166299701-166300578	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:166298064..166301679-chr4:166306197..166309667,4	MCF-7	breast:
2	chr4:166126423..166128941-chr4:166299614..166301287,2	MCF-7	breast:
3	chr4:166298593..166300612-chr4:166306180..166307966,2	MCF-7	breast:

Variant related genes	Relation type
CPE	TF binding region
ENSG00000207559	Chromatin interaction
ENSG00000109466	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12506365	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13106028	1.00[ASN][1000 genomes]
rs13137171	1.00[ASN][1000 genomes]
rs4690813	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4691187	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6536907	1.00[ASN][1000 genomes]
rs6536908	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6842704	1.00[ASN][1000 genomes]
rs7671176	1.00[ASN][1000 genomes]
rs7677572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7696111	0.82[ASN][1000 genomes]
rs934814	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166298000-166302400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:166299000-166300000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:166299200-166300000	Flanking Active TSS	HepG2	liver
4	chr4:166299200-166301000	Active TSS	Colon Smooth Muscle	Colon
5	chr4:166299200-166301400	Active TSS	Rectal Smooth Muscle	rectum
6	chr4:166299200-166303200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:166299400-166300000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:166299400-166300000	Flanking Active TSS	Brain Angular Gyrus	brain
9	chr4:166299400-166300000	Flanking Active TSS	Brain Cingulate Gyrus	brain
10	chr4:166299400-166301000	Active TSS	Brain Germinal Matrix	brain
11	chr4:166299400-166301400	Active TSS	Stomach Smooth Muscle	stomach
12	chr4:166299400-166302200	Active TSS	Aorta	Aorta
13	chr4:166299400-166304000	Active TSS	Brain Hippocampus Middle	brain
14	chr4:166299600-166300000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
15	chr4:166299600-166300000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr4:166299600-166300000	Flanking Active TSS	Fetal Lung	lung
17	chr4:166299600-166300000	Active TSS	Right Atrium	heart
18	chr4:166299600-166300000	Flanking Bivalent TSS/Enh	A549	lung
19	chr4:166299600-166300000	Flanking Active TSS	HMEC	breast
20	chr4:166299600-166300200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:166299600-166300200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:166299600-166300200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:166299600-166300200	Flanking Active TSS	HUVEC	blood vessel
24	chr4:166299600-166300400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:166299600-166300600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
26	chr4:166299600-166300600	Bivalent/Poised TSS	NHEK	skin
27	chr4:166299600-166300800	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr4:166299600-166300800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:166299600-166300800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
30	chr4:166299600-166300800	Active TSS	Fetal Brain Male	brain
31	chr4:166299600-166300800	Bivalent/Poised TSS	Osteobl	bone
32	chr4:166299600-166301000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr4:166299600-166301000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr4:166299600-166301200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:166299600-166301200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr4:166299600-166301200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:166299600-166301200	Active TSS	Ovary	ovary
38	chr4:166299600-166301200	Bivalent/Poised TSS	Thymus	Thymus
39	chr4:166299600-166301400	Active TSS	NH-A	brain
40	chr4:166299600-166301400	Active TSS	NHLF	lung
41	chr4:166299600-166301600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:166299600-166301600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:166299600-166301800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr4:166299600-166304400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr4:166299800-166300000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:166299800-166300000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:166299800-166300000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:166299800-166300000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr4:166299800-166300000	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:166299800-166300000	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links