Variant report

Variant	rs11129128
Chromosome Location	chr3:23961621-23961622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:104)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:104 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr3:23961122-23963134	K562	blood:	n/a	n/a
2	POLR2A	chr3:23961148-23964111	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:23961248-23962118	HEK293	kidney:	n/a	n/a
4	POLR2A	chr3:23961440-23962090	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:23961138-23963839	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:23961371-23963855	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:23961180-23964553	GM12891	blood:	n/a	n/a
9	HEY1	chr3:23961137-23962192	K562	blood:	n/a	n/a
10	POLR2A	chr3:23961503-23963863	K562	blood:	n/a	n/a
11	POLR2A	chr3:23961166-23963865	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:23958006-23962277	GM12878	blood:	n/a	n/a
13	STAT5A	chr3:23961566-23962161	GM12878	blood:	n/a	n/a
14	MBD4	chr3:23961405-23963188	HepG2	liver:	n/a	n/a
15	NFATC1	chr3:23961447-23963282	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:23957976-23965870	K562	blood:	n/a	n/a
17	PML	chr3:23961233-23962252	K562	blood:	n/a	n/a
18	POLR2A	chr3:23957870-23963941	H1-hESC	embryonic stem cell:	n/a	n/a
19	PML	chr3:23961388-23963850	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:23961064-23963934	K562	blood:	n/a	n/a
21	ATF2	chr3:23961592-23963025	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:23961218-23963277	HL-60	blood:	n/a	n/a
23	HEY1	chr3:23961236-23962079	K562	blood:	n/a	n/a
24	ATF2	chr3:23961107-23963189	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:23961309-23963207	PBDE	blood:	n/a	n/a
26	POLR2A	chr3:23961267-23963083	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:23961272-23963810	GM18951	blood:	n/a	n/a
28	POLR2A	chr3:23961184-23963270	HCT-116	colon:	n/a	n/a
29	POLR2A	chr3:23961210-23962212	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:23960818-23964110	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:23961089-23963277	U87	brain:	n/a	n/a
32	POLR2A	chr3:23961251-23963895	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:23960446-23964170	HepG2	liver:	n/a	n/a
34	BCL3	chr3:23961412-23963239	A549	lung:	n/a	n/a
35	POLR2A	chr3:23961243-23963280	Hela-S3	cervix:	n/a	n/a
36	BCLAF1	chr3:23961559-23962097	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:23961202-23962157	HL-60	blood:	n/a	n/a
38	POLR2A	chr3:23961220-23963903	K562	blood:	n/a	n/a
39	POLR2A	chr3:23961218-23962256	GM12891	blood:	n/a	n/a
40	POLR2A	chr3:23961404-23962206	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr3:23961181-23962213	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:23961348-23962286	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:23961260-23963885	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:23961237-23962236	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr3:23961129-23963278	K562	blood:	n/a	n/a
46	POLR2A	chr3:23961614-23962105	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr3:23961148-23963817	K562	blood:	n/a	n/a
48	POLR2A	chr3:23961114-23963096	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:23961200-23963833	GM12892	blood:	n/a	n/a
50	POLR2A	chr3:23961188-23963900	GM18505	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23960526..23962863-chr3:24013920..24016141,2	K562	blood:
2	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
3	chr3:23960619..23962438-chr3:24535920..24537440,2	MCF-7	breast:
4	chr3:23051768..23053551-chr3:23960276..23962039,2	K562	blood:
5	chr3:23961179..23963059-chr3:24534695..24537090,2	K562	blood:
6	chr3:23931925..23934532-chr3:23961376..23962926,2	MCF-7	breast:
7	chr3:23748425..23751412-chr3:23960441..23962908,2	K562	blood:
8	chr3:23960922..23962761-chr3:24002838..24004607,2	K562	blood:
9	chr3:23905396..23907030-chr3:23960105..23962888,2	K562	blood:
10	chr3:23961544..23965594-chr3:24039129..24042717,4	K562	blood:
11	chr3:23928269..23930887-chr3:23960946..23963532,2	MCF-7	breast:
12	chr3:23846543..23848626-chr3:23961090..23963497,2	K562	blood:
13	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
14	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
15	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
16	chr3:23960325..23963916-chr3:24723703..24727555,4	MCF-7	breast:

No data

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000151090	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10084748	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11129130	0.82[YRI][hapmap]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs13321439	0.87[EUR][1000 genomes]
rs13321440	0.87[EUR][1000 genomes]
rs1533141	0.85[EUR][1000 genomes]
rs1567579	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.87[EUR][1000 genomes]
rs34866549	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35755171	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	0.86[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.86[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6776568	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6778577	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6790140	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71324126	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150266	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7611018	1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs954748	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs9812870	0.96[EUR][1000 genomes]
rs9817923	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9853954	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863176	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883834	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv1067849	chr3:23960157-23962549	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23958800-23962000	Transcr. at gene 5' and 3'	A549	lung
2	chr3:23959000-23962000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:23959200-23961800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:23959200-23961800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
5	chr3:23959200-23961800	Transcr. at gene 5' and 3'	K562	blood
6	chr3:23959200-23962000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
7	chr3:23959400-23961800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
8	chr3:23959400-23962000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:23959600-23962000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:23959600-23962200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:23959600-23962200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr3:23959600-23965200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:23959600-23965600	Weak transcription	Spleen	Spleen
14	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:23959800-23965000	Weak transcription	Ovary	ovary
16	chr3:23960000-23962000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:23960000-23965000	Weak transcription	Colonic Mucosa	Colon
18	chr3:23960200-23961800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:23960200-23961800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:23960200-23962000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:23960200-23962000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:23960200-23962000	Strong transcription	Small Intestine	intestine
23	chr3:23960200-23962200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:23960200-23963000	Genic enhancers	Primary B cells from cord blood	blood
25	chr3:23960200-23964400	Strong transcription	Placenta	Placenta
26	chr3:23960200-23967000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:23960200-23969400	Weak transcription	Esophagus	oesophagus
28	chr3:23960400-23961800	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr3:23960400-23961800	Enhancers	Fetal Heart	heart
30	chr3:23960400-23961800	Genic enhancers	Fetal Lung	lung
31	chr3:23960400-23962000	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr3:23960400-23962200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:23960400-23963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:23960400-23963800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:23960400-23963800	Strong transcription	Brain Hippocampus Middle	brain
36	chr3:23960400-23963800	Strong transcription	Thymus	Thymus
37	chr3:23960400-23964200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:23960400-23964600	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:23960600-23961800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:23960600-23961800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:23960600-23961800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
42	chr3:23960600-23962000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:23960600-23962000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:23960600-23962000	Genic enhancers	Primary T cells from cord blood	blood
45	chr3:23960600-23962000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:23960600-23962000	Strong transcription	Brain Substantia Nigra	brain
47	chr3:23960600-23962000	Genic enhancers	Colon Smooth Muscle	Colon
48	chr3:23960600-23962000	Genic enhancers	Fetal Brain Male	brain
49	chr3:23960600-23962000	Genic enhancers	Fetal Brain Female	brain
50	chr3:23960600-23962200	Strong transcription	H9 Cell Line	embryonic stem cell

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