Variant report

Variant	rs485789
Chromosome Location	chr3:159730148-159730149
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	ELK1	chr3:159729951-159730212	GM12878	blood:	n/a	n/a
2	CHD2	chr3:159729901-159730629	GM12878	blood:	n/a	n/a
3	SPI1	chr3:159729758-159730335	GM12891	blood:	n/a	chr3:159730049-159730058
4	EP300	chr3:159729743-159730350	GM12878	blood:	n/a	chr3:159730049-159730063
5	SMC3	chr3:159729933-159730258	GM12878	blood:	n/a	n/a
6	EP300	chr3:159729814-159730326	GM12878	blood:	n/a	chr3:159730049-159730063
7	MEF2A	chr3:159729790-159730284	GM12878	blood:	n/a	chr3:159730051-159730059 chr3:159730123-159730138
8	POU2F2	chr3:159729908-159730185	GM12878	blood:	n/a	chr3:159729917-159729932 chr3:159729915-159729930
9	EBF1	chr3:159729898-159730316	GM12878	blood:	n/a	n/a
10	ATF2	chr3:159729781-159730314	GM12878	blood:	n/a	n/a
11	STAT1	chr3:159729969-159730177	GM12878	blood:	n/a	chr3:159730047-159730058
12	EBF1	chr3:159729924-159730176	GM12878	blood:	n/a	n/a
13	CUX1	chr3:159729635-159730249	GM12878	blood:	n/a	n/a
14	NFYB	chr3:159730096-159730303	GM12878	blood:	n/a	n/a
15	IRF4	chr3:159729741-159730344	GM12878	blood:	n/a	n/a
16	NFIC	chr3:159729687-159730391	GM12878	blood:	n/a	n/a
17	NFIC	chr3:159729741-159730415	GM12878	blood:	n/a	n/a
18	PML	chr3:159729743-159730374	GM12878	blood:	n/a	n/a
19	ATF2	chr3:159729767-159730313	GM12878	blood:	n/a	n/a
20	SPI1	chr3:159729863-159730197	GM12878	blood:	n/a	chr3:159730049-159730058
21	USF2	chr3:159729879-159730249	GM12878	blood:	n/a	n/a
22	MTA3	chr3:159729747-159730417	GM12878	blood:	n/a	n/a
23	RELA	chr3:159729645-159730280	GM12878	blood:	n/a	n/a
24	BATF	chr3:159729908-159730310	GM12878	blood:	n/a	n/a
25	MXI1	chr3:159729812-159730587	GM12878	blood:	n/a	n/a
26	BCL11A	chr3:159729912-159730274	GM12878	blood:	n/a	chr3:159730049-159730058
27	SP1	chr3:159729915-159730264	GM12878	blood:	n/a	n/a
28	NFATC1	chr3:159729794-159730325	GM12878	blood:	n/a	n/a
29	RFX5	chr3:159729917-159730180	GM12878	blood:	n/a	n/a
30	CHD1	chr3:159729890-159730483	GM12878	blood:	n/a	n/a
31	BCL11A	chr3:159729843-159730281	GM12878	blood:	n/a	chr3:159730049-159730058
32	BCLAF1	chr3:159729793-159730278	GM12878	blood:	n/a	chr3:159730049-159730058
33	SPI1	chr3:159729540-159730584	GM12878	blood:	n/a	chr3:159730049-159730058
34	BCLAF1	chr3:159729804-159730250	GM12878	blood:	n/a	chr3:159730049-159730058
35	FOXM1	chr3:159729775-159730261	GM12878	blood:	n/a	n/a
36	ZNF384	chr3:159729764-159730152	GM12878	blood:	n/a	n/a
37	RUNX3	chr3:159729777-159730363	GM12878	blood:	n/a	n/a
38	SPI1	chr3:159729812-159730276	GM12878	blood:	n/a	chr3:159730049-159730058
39	SPI1	chr3:159729814-159730289	GM12891	blood:	n/a	chr3:159730049-159730058
40	IKZF1	chr3:159729727-159730733	GM12878	blood:	n/a	n/a
41	PAX5	chr3:159729759-159730327	GM12878	blood:	n/a	chr3:159730049-159730058
42	BCL3	chr3:159729862-159730261	GM12878	blood:	n/a	chr3:159730049-159730058
43	RCOR1	chr3:159729837-159730390	GM12878	blood:	n/a	n/a
44	MAX	chr3:159729850-159730331	GM12878	blood:	n/a	chr3:159730028-159730039
45	TBL1XR1	chr3:159729793-159730341	GM12878	blood:	n/a	n/a
46	BHLHE40	chr3:159729679-159730746	GM12878	blood:	n/a	n/a
47	RUNX3	chr3:159729891-159730333	GM12878	blood:	n/a	n/a
48	EP300	chr3:159729852-159730312	GM12878	blood:	n/a	chr3:159730049-159730063
49	STAT3	chr3:159729703-159730250	GM12878	blood:	n/a	chr3:159730047-159730058
50	WRNIP1	chr3:159729687-159730172	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LINC01100	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11708713	0.96[EUR][1000 genomes]
rs11716424	0.96[EUR][1000 genomes]
rs11716451	0.96[EUR][1000 genomes]
rs1651081	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1874886	0.96[EUR][1000 genomes]
rs2366643	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2366644	0.94[EUR][1000 genomes]
rs2647928	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2647930	0.96[EUR][1000 genomes]
rs2647931	0.96[EUR][1000 genomes]
rs2914116	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2936302	0.95[EUR][1000 genomes]
rs2936303	0.96[EUR][1000 genomes]
rs4580600	0.94[EUR][1000 genomes]
rs4679867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680536	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680538	0.94[EUR][1000 genomes]
rs480134	0.95[EUR][1000 genomes]
rs480913	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs483714	0.96[EUR][1000 genomes]
rs484600	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs485499	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491966	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs522127	0.96[EUR][1000 genomes]
rs523886	0.96[EUR][1000 genomes]
rs526734	0.93[EUR][1000 genomes]
rs545143	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs545232	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs547875	0.96[EUR][1000 genomes]
rs548018	0.96[EUR][1000 genomes]
rs55740284	0.93[ASN][1000 genomes]
rs564799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571099	0.96[EUR][1000 genomes]
rs574808	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs579079	0.97[EUR][1000 genomes]
rs586094	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs587422	0.96[EUR][1000 genomes]
rs588998	0.96[EUR][1000 genomes]
rs589446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589545	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs600519	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs62270441	0.96[EUR][1000 genomes]
rs629209	0.96[EUR][1000 genomes]
rs6441288	1.00[CEU][hapmap]
rs6441289	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6441290	0.96[EUR][1000 genomes]
rs669003	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs6771363	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6808498	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6808518	0.96[EUR][1000 genomes]
rs7640862	0.94[EUR][1000 genomes]
rs9290051	0.94[EUR][1000 genomes]
rs9845010	0.96[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	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1806743	chr3:159723529-159744022	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs485789	SCHIP1	cis	lymphoblastoid	seeQTL
rs485789	IL12A	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159713000-159734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:159726600-159731000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:159728600-159730800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:159729200-159730200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:159729200-159740800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:159729400-159730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:159729400-159730800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:159729600-159730400	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:159729600-159730400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:159729600-159730800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:159729600-159730800	Flanking Active TSS	GM12878-XiMat	blood
12	chr3:159729800-159730200	Enhancers	Osteobl	bone
13	chr3:159729800-159730600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:159730000-159730200	Enhancers	Primary B cells from cord blood	blood
15	chr3:159730000-159730400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:159730000-159730400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:159730000-159730600	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links