Variant report

Variant	rs1492483
Chromosome Location	chr3:111847985-111847986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr3:111846287-111853296	GM12878	blood:	n/a	n/a
2	POU2F2	chr3:111847784-111848016	GM12878	blood:	n/a	n/a
3	YY1	chr3:111847756-111848032	GM12878	blood:	n/a	n/a
4	TCF12	chr3:111847701-111848074	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:111846191-111854054	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:111846327-111850616	GM12891	blood:	n/a	n/a
7	STAT5A	chr3:111846153-111850352	GM12878	blood:	n/a	n/a
8	PAX5	chr3:111847682-111848070	GM12878	blood:	n/a	n/a
9	TCF3	chr3:111847688-111848108	GM12878	blood:	n/a	n/a
10	SPI1	chr3:111847697-111848150	HL-60	blood:	n/a	n/a
11	EBF1	chr3:111847678-111848099	GM12878	blood:	n/a	n/a
12	EBF1	chr3:111846296-111848395	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:111847739-111848090	GM12878	blood:	n/a	n/a
14	BCLAF1	chr3:111847282-111850673	GM12878	blood:	n/a	n/a
15	MYC	chr3:111847915-111848471	MCF10A-Er-Src	breast:	n/a	n/a
16	ATF2	chr3:111847417-111848336	GM12878	blood:	n/a	n/a
17	SPI1	chr3:111847760-111848106	GM12878	blood:	n/a	n/a
18	CEBPB	chr3:111846236-111848344	GM12878	blood:	n/a	n/a
19	FOS	chr3:111847886-111847995	MCF10A-Er-Src	breast:	n/a	n/a
20	SPI1	chr3:111847835-111848046	GM12878	blood:	n/a	n/a
21	STAT1	chr3:111847662-111848235	GM12878	blood:	n/a	n/a
22	SPI1	chr3:111847764-111848075	GM12891	blood:	n/a	n/a
23	POLR2A	chr3:111846304-111850588	GM12878	blood:	n/a	n/a
24	EP300	chr3:111847561-111848338	GM12878	blood:	n/a	n/a
25	CUX1	chr3:111847524-111848144	GM12878	blood:	n/a	n/a
26	TAF1	chr3:111847723-111847995	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:111846299-111854337	Raji	blood:	n/a	n/a
28	NFATC1	chr3:111846108-111854042	GM12878	blood:	n/a	n/a
29	CHD2	chr3:111846255-111849775	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:111847278-111850662	GM12891	blood:	n/a	n/a
31	SPI1	chr3:111847755-111848113	GM12891	blood:	n/a	n/a
32	MEF2A	chr3:111847475-111848105	GM12878	blood:	n/a	n/a
33	TAF1	chr3:111847753-111848024	GM12891	blood:	n/a	n/a
34	PAX5	chr3:111847733-111848001	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:111846326-111850640	GM12892	blood:	n/a	n/a
36	FOXM1	chr3:111847466-111848662	GM12878	blood:	n/a	n/a
37	NFIC	chr3:111845900-111853068	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:111846294-111850516	GM12878	blood:	n/a	n/a
39	JUND	chr3:111847840-111848096	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr3:111846273-111849806	GM12878	blood:	n/a	n/a
41	PML	chr3:111847292-111848067	GM12878	blood:	n/a	n/a
42	STAT3	chr3:111846351-111848355	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:111846063-111856284	GM12878	blood:	n/a	n/a
44	POU2F2	chr3:111847614-111848489	GM12878	blood:	n/a	n/a
45	IRF1	chr3:111847942-111848136	K562	blood:	n/a	n/a
46	FOXM1	chr3:111847537-111849491	GM12878	blood:	n/a	n/a
47	TBP	chr3:111847331-111848429	GM12878	blood:	n/a	n/a
48	MYC	chr3:111847901-111848585	MCF10A-Er-Src	breast:	n/a	n/a
49	TBL1XR1	chr3:111846204-111850317	GM12878	blood:	n/a	n/a
50	BCL3	chr3:111847582-111848097	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111847880..111850020-chr3:111853363..111855943,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261488	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10511306	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10511307	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs11928130	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13059342	0.81[CHB][hapmap]
rs13069933	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13078713	0.90[CHB][hapmap]
rs1388855	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1492480	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492481	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492484	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492485	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492486	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1602672	0.89[ASN][1000 genomes]
rs1948404	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1994772	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029638	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651558	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879652	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs950528	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1492483	CD200	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
2	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
3	chr3:111830600-111853200	Weak transcription	Lung	lung
4	chr3:111834200-111853800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:111834400-111848000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:111835800-111849600	Weak transcription	Small Intestine	intestine
7	chr3:111836200-111849200	Weak transcription	Aorta	Aorta
8	chr3:111839000-111853000	Weak transcription	Left Ventricle	heart
9	chr3:111840800-111849200	Weak transcription	Gastric	stomach
10	chr3:111840800-111855800	Weak transcription	NH-A	brain
11	chr3:111842800-111849200	Weak transcription	Pancreas	Pancrea
12	chr3:111843600-111848400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:111843600-111848400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:111843600-111849200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:111843600-111849800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
16	chr3:111843800-111848400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:111843800-111849000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:111843800-111849200	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:111844000-111848600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:111844000-111848800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:111844400-111850000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:111844800-111848800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:111844800-111855800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:111845000-111851000	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:111845400-111848600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:111845600-111850800	Weak transcription	HSMMtube	muscle
27	chr3:111845600-111852800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:111845600-111855800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:111845800-111851800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:111845800-111853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:111846000-111850200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:111846200-111849400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:111846400-111850800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:111846600-111848600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr3:111846600-111849200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:111846600-111849200	Enhancers	Fetal Thymus	thymus
37	chr3:111846800-111848000	Enhancers	Duodenum Mucosa	Duodenum
38	chr3:111846800-111848600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:111846800-111848800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:111846800-111849000	Enhancers	Thymus	Thymus
41	chr3:111846800-111850800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr3:111846800-111851600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:111846800-111853000	Weak transcription	Adipose Nuclei	Adipose
44	chr3:111847000-111848200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:111847000-111848200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:111847000-111848400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:111847000-111849000	Enhancers	Primary T cells from cord blood	blood
48	chr3:111847000-111849200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:111847000-111849400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:111847000-111849600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links