Variant report

Variant	rs2286487
Chromosome Location	chr3:45883711-45883712
allele	A/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	MTA3	chr3:45882896-45884096	GM12878	blood:	n/a	n/a
2	GABPA	chr3:45883274-45883933	HepG2	liver:	n/a	chr3:45883710-45883719
3	CEBPB	chr3:45883257-45884031	MCF-7	breast:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
4	TCF12	chr3:45883168-45884088	ECC-1	luminal epithelium:	n/a	chr3:45883363-45883370
5	EP300	chr3:45883522-45883897	GM12878	blood:	n/a	chr3:45883733-45883740
6	POLR2A	chr3:45883390-45883944	HepG2	liver:	n/a	n/a
7	MXI1	chr3:45882841-45884011	GM12878	blood:	n/a	n/a
8	SP2	chr3:45883506-45883953	H1-hESC	embryonic stem cell:	n/a	chr3:45883655-45883665
9	POLR2A	chr3:45883016-45883858	IMR90	lung:	n/a	n/a
10	SIN3AK20	chr3:45883195-45884049	HCT-116	colon:	n/a	n/a
11	NFIC	chr3:45883403-45883915	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:45883491-45883952	SK-N-SH	brain:	n/a	n/a
13	MAX	chr3:45883118-45884158	HCT-116	colon:	n/a	chr3:45883629-45883639
14	ATF3	chr3:45883506-45883892	K562	blood:	n/a	n/a
15	MAX	chr3:45883172-45884148	A549	lung:	n/a	chr3:45883629-45883639
16	USF2	chr3:45883283-45883938	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:45883316-45883969	HepG2	liver:	n/a	n/a
18	E2F6	chr3:45883514-45884038	A549	lung:	n/a	n/a
19	E2F6	chr3:45883252-45884142	A549	lung:	n/a	n/a
20	POLR2A	chr3:45883512-45883981	PANC-1	pancreas:	n/a	n/a
21	PML	chr3:45883578-45883893	GM12878	blood:	n/a	n/a
22	SETDB1	chr3:45883222-45884060	K562	blood:	n/a	n/a
23	SIN3A	chr3:45883084-45883986	GM12878	blood:	n/a	n/a
24	MAX	chr3:45882904-45883965	NB4	blood:	n/a	chr3:45883629-45883639
25	GABPA	chr3:45883106-45884267	HL-60	blood:	n/a	chr3:45883710-45883719
26	ATF3	chr3:45883443-45883757	HepG2	liver:	n/a	n/a
27	GTF2F1	chr3:45883531-45883993	Hela-S3	cervix:	n/a	n/a
28	GABPA	chr3:45883329-45884161	MCF-7	breast:	n/a	chr3:45883710-45883719
29	SIN3AK20	chr3:45883365-45883918	A549	lung:	n/a	n/a
30	POLR2A	chr3:45883289-45884027	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr3:45883691-45883866	A549	lung:	n/a	n/a
32	CEBPB	chr3:45883309-45884107	ECC-1	luminal epithelium:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
33	MXI1	chr3:45882091-45884476	IMR90	lung:	n/a	n/a
34	TEAD4	chr3:45883408-45883797	K562	blood:	n/a	n/a
35	CBX3	chr3:45883409-45884028	K562	blood:	n/a	n/a
36	MAX	chr3:45883370-45884126	MCF-7	breast:	n/a	chr3:45883629-45883639
37	GABPA	chr3:45882737-45884433	MCF-7	breast:	n/a	chr3:45883018-45883027 chr3:45883016-45883030 chr3:45883710-45883719
38	RCOR1	chr3:45883374-45884031	GM12878	blood:	n/a	n/a
39	NFYA	chr3:45883220-45883904	K562	blood:	n/a	chr3:45883649-45883667
40	RAD21	chr3:45882759-45883934	IMR90	lung:	n/a	n/a
41	GABPA	chr3:45883082-45884217	SK-N-SH	brain:	n/a	chr3:45883710-45883719
42	NRF1	chr3:45883531-45883845	K562	blood:	n/a	chr3:45883710-45883719 chr3:45883708-45883719
43	GABPA	chr3:45883209-45884156	SK-N-SH	brain:	n/a	chr3:45883710-45883719
44	POLR2A	chr3:45883427-45884022	SK-N-SH	brain:	n/a	n/a
45	ELK1	chr3:45883251-45883893	K562	blood:	n/a	n/a
46	SP1	chr3:45883407-45883880	HepG2	liver:	n/a	chr3:45883646-45883667
47	FOS	chr3:45883549-45883859	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:45883332-45884040	HCT-116	colon:	n/a	n/a
49	POLR2A	chr3:45883219-45883908	K562	blood:	n/a	n/a
50	GABPA	chr3:45883419-45884105	HL-60	blood:	n/a	chr3:45883710-45883719

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:45883676-45883726	HAEpiC	amniotic membrane:	n/a
2	chr3:45883676-45883726	AG10803	skin:	n/a
3	chr3:45883693-45883743	ProgFib	skin:	n/a
4	chr3:45883676-45883726	GM12878	blood:	n/a
5	chr3:45883693-45883743	HAEpiC	amniotic membrane:	n/a
6	chr3:45883693-45883743	HEEpiC	esophagus:	n/a
7	chr3:45883693-45883743	BJ	skin:	n/a
8	chr3:45883693-45883743	NHBE	bronchial:	n/a
9	chr3:45883676-45883726	HEEpiC	esophagus:	n/a
10	chr3:45883676-45883726	HNPCEpiC	eye:	n/a
11	chr3:45883693-45883743	GM12892	blood:	n/a
12	chr3:45883693-45883743	HRE	kidney:	n/a
13	chr3:45883693-45883743	NHDF-neo	bronchial:	n/a
14	chr3:45883676-45883726	NHDF-neo	bronchial:	n/a
15	chr3:45883676-45883726	PANC-1	pancreas:	n/a
16	chr3:45883693-45883743	CMK	blood:	n/a
17	chr3:45883693-45883743	GM06990	blood:	n/a
18	chr3:45883676-45883726	GM12891	blood:	n/a
19	chr3:45883676-45883726	NHBE	bronchial:	n/a
20	chr3:45883693-45883743	GM12878	blood:	n/a
21	chr3:45883693-45883743	GM19239	blood:	n/a
22	chr3:45883676-45883726	AG04450	lung:	fetal
23	chr3:45883676-45883726	HIPEpiC	eye:	n/a
24	chr3:45883693-45883743	A549	lung:	n/a
25	chr3:45883693-45883743	RPTEC	kidney:	n/a
26	chr3:45883676-45883726	LNCaP	prostate:	n/a
27	chr3:45883693-45883743	MCF10A-Er-Src	breast:	n/a
28	chr3:45883693-45883743	HEK293	kidney:	embryo
29	chr3:45883676-45883726	HCT-116	colon:	n/a
30	chr3:45883676-45883726	SK-N-SH	brain:	n/a
31	chr3:45883693-45883743	AG04449	skin:	fetal
32	chr3:45883693-45883743	H1-hESC	embryonic stem cell:	embryo
33	chr3:45883693-45883743	MCF-7	breast:	n/a
34	chr3:45883676-45883726	PFSK-1	brain:	n/a
35	chr3:45883676-45883726	NB4	blood:	n/a
36	chr3:45883693-45883743	HCF	heart:	n/a
37	chr3:45883693-45883743	SK-N-SH_RA	brain:	n/a
38	chr3:45883693-45883743	ECC-1	luminal epithelium:	n/a
39	chr3:45883693-45883743	PANC-1	pancreas:	n/a
40	chr3:45883676-45883726	HepG2	liver:	n/a
41	chr3:45883693-45883743	LNCaP	prostate:	n/a
42	chr3:45883693-45883743	NT2-D1	testis:	n/a
43	chr3:45883693-45883743	AG10803	skin:	n/a
44	chr3:45883693-45883743	PFSK-1	brain:	n/a
45	chr3:45883693-45883743	HRPEpiC	eye:	n/a
46	chr3:45883676-45883726	Hela-S3	cervix:	n/a
47	chr3:45883676-45883726	ProgFib	skin:	n/a
48	chr3:45883693-45883743	Hela-S3	cervix:	n/a
49	chr3:45883693-45883743	U87	brain:	n/a
50	chr3:45883693-45883743	HCM	heart:	n/a

Variant related genes	Relation type
LZTFL1	TF binding region
LZTFL1	CpG island

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11130077	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1129183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318088	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488370	0.81[ASN][1000 genomes]
rs1883091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531756	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742364	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742365	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774643	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774644	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45558831	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683143	0.96[ASN][1000 genomes]
rs60103812	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61157369	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836780	1.00[YRI][hapmap]
rs9844499	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849511	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882270	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45882200-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:45882200-45884000	Active TSS	Thymus	Thymus
3	chr3:45882200-45884200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:45882200-45886600	Strong transcription	Dnd41	blood
5	chr3:45882400-45883800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:45882400-45884000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:45882400-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:45882400-45884200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr3:45882400-45884400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:45882600-45883800	Active TSS	Fetal Intestine Large	intestine
11	chr3:45882600-45883800	Active TSS	Fetal Muscle Trunk	muscle
12	chr3:45882600-45883800	Active TSS	Left Ventricle	heart
13	chr3:45882600-45884000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:45882600-45884000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr3:45882600-45884000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:45882600-45884000	Active TSS	Ovary	ovary
17	chr3:45882600-45884200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:45882600-45884200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:45882600-45884200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr3:45882600-45884200	Active TSS	Right Atrium	heart
21	chr3:45882600-45884200	Active TSS	A549	lung
22	chr3:45882600-45884200	Active TSS	HSMM	muscle
23	chr3:45882600-45884400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr3:45882800-45883800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr3:45882800-45883800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:45882800-45883800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:45882800-45883800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:45882800-45883800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:45882800-45883800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:45882800-45883800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:45882800-45883800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:45882800-45883800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:45882800-45883800	Active TSS	Brain Anterior Caudate	brain
34	chr3:45882800-45883800	Active TSS	Brain Hippocampus Middle	brain
35	chr3:45882800-45883800	Active TSS	Colon Smooth Muscle	Colon
36	chr3:45882800-45883800	Active TSS	Lung	lung
37	chr3:45882800-45883800	Active TSS	HepG2	liver
38	chr3:45882800-45883800	Active TSS	NHLF	lung
39	chr3:45882800-45884000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr3:45882800-45884000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:45882800-45884000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:45882800-45884000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:45882800-45884000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:45882800-45884000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:45882800-45884000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:45882800-45884000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr3:45882800-45884000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:45882800-45884000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:45882800-45884000	Active TSS	Brain Angular Gyrus	brain
50	chr3:45882800-45884000	Active TSS	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links