Variant report

Variant	rs879652
Chromosome Location	chr3:111851890-111851891
allele	A/G
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	NFATC1	chr3:111846287-111853296	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:111850784-111853964	GM12891	blood:	n/a	n/a
3	SPI1	chr3:111851728-111852351	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:111850883-111854136	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:111851381-111852487	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:111846191-111854054	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:111851657-111852301	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr3:111851772-111852339	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:111851559-111852316	GM18951	blood:	n/a	n/a
10	WRNIP1	chr3:111850971-111852299	GM12878	blood:	n/a	n/a
11	EBF1	chr3:111851012-111856368	GM12878	blood:	n/a	chr3:111852245-111852256
12	YY1	chr3:111851816-111852407	GM12892	blood:	n/a	n/a
13	POU2F2	chr3:111851763-111852269	GM12878	blood:	n/a	n/a
14	MAZ	chr3:111850037-111852643	GM12878	blood:	n/a	chr3:111852319-111852327 chr3:111852129-111852139
15	RUNX3	chr3:111850936-111853979	GM12878	blood:	n/a	n/a
16	EP300	chr3:111851070-111854042	GM12878	blood:	n/a	chr3:111851867-111851881 chr3:111851873-111851887 chr3:111852008-111852017
17	EBF1	chr3:111851612-111852509	GM12878	blood:	n/a	chr3:111852245-111852256
18	YY1	chr3:111851831-111852332	GM12891	blood:	n/a	n/a
19	PML	chr3:111850554-111854266	GM12878	blood:	n/a	chr3:111852106-111852114
20	STAT5A	chr3:111850377-111854015	GM12878	blood:	n/a	chr3:111851865-111851876 chr3:111851072-111851092 chr3:111851295-111851306
21	STAT1	chr3:111851663-111852430	GM12878	blood:	n/a	chr3:111851865-111851876
22	TAF1	chr3:111851710-111852300	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:111851008-111852379	GM19193	blood:	n/a	n/a
24	E2F4	chr3:111851768-111852781	GM12878	blood:	n/a	n/a
25	MEF2A	chr3:111851801-111852467	GM12878	blood:	n/a	n/a
26	RELA	chr3:111851600-111852705	GM19099	blood:	n/a	n/a
27	BCL3	chr3:111851741-111852502	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
28	RELA	chr3:111851497-111852862	GM10847	blood:	n/a	n/a
29	SPI1	chr3:111851821-111852290	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:111850789-111854058	GM12892	blood:	n/a	n/a
31	ELK1	chr3:111851768-111852554	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:111850717-111854239	GM12892	blood:	n/a	n/a
33	ETS1	chr3:111851743-111852272	GM12878	blood:	n/a	chr3:111852133-111852144
34	TBP	chr3:111848676-111853001	GM12878	blood:	n/a	n/a
35	MEF2C	chr3:111851677-111852524	GM12878	blood:	n/a	n/a
36	IRF4	chr3:111851680-111852419	GM12878	blood:	n/a	n/a
37	BCLAF1	chr3:111850867-111854010	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
38	CEBPB	chr3:111850869-111852835	GM12878	blood:	n/a	n/a
39	FOXM1	chr3:111850668-111852993	GM12878	blood:	n/a	n/a
40	RCOR1	chr3:111850970-111852701	GM12878	blood:	n/a	n/a
41	POU2F2	chr3:111851411-111852396	GM12878	blood:	n/a	n/a
42	PAX5	chr3:111851346-111852464	GM12878	blood:	n/a	chr3:111851873-111851882
43	RELA	chr3:111851431-111853146	GM12878	blood:	n/a	n/a
44	EP300	chr3:111851540-111852675	GM12878	blood:	n/a	chr3:111851867-111851881 chr3:111851873-111851887 chr3:111852008-111852017
45	TAF1	chr3:111851794-111852334	GM12891	blood:	n/a	n/a
46	POLR2A	chr3:111850956-111853341	GM19099	blood:	n/a	n/a
47	TBL1XR1	chr3:111850671-111854123	GM12878	blood:	n/a	n/a
48	PAX5	chr3:111851859-111852336	GM12878	blood:	n/a	chr3:111851873-111851882
49	POLR2A	chr3:111850835-111853668	GM12878	blood:	n/a	n/a
50	RFX5	chr3:111851827-111852821	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000261488	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10511306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10511308	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs10934156	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs11919901	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs11924882	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs11926448	0.83[AFR][1000 genomes]
rs11928130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053863	0.95[CEU][hapmap]
rs13059342	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap]
rs13061801	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs13069933	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077603	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs13078713	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs13079706	0.82[CEU][hapmap]
rs13080696	0.81[AFR][1000 genomes]
rs13087387	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs13089316	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs13090344	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1388855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1492480	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1492481	0.94[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492483	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492485	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492486	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586874	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1602672	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1948404	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1994772	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029638	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34043603	0.83[AFR][1000 genomes]
rs35411358	0.87[EUR][1000 genomes]
rs4279069	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs4564948	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs4682100	1.00[YRI][hapmap]
rs4682389	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs6781137	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7651558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs950528	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

No data

Chromatin state (count:72 , 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	chr3:111839000-111853000	Weak transcription	Left Ventricle	heart
6	chr3:111840800-111855800	Weak transcription	NH-A	brain
7	chr3:111844800-111855800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:111845600-111852800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:111845600-111855800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:111845800-111853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:111846800-111853000	Weak transcription	Adipose Nuclei	Adipose
12	chr3:111847000-111853200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:111848000-111853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:111848200-111857000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:111848400-111853800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:111848400-111854600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:111848400-111854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:111848400-111855800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:111848400-111856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:111848400-111856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:111848800-111853600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:111848800-111854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:111849000-111854800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:111849200-111853000	Weak transcription	Hela-S3	cervix
25	chr3:111849200-111855000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:111849800-111852400	Active TSS	GM12878-XiMat	blood
27	chr3:111849800-111852600	Weak transcription	Gastric	stomach
28	chr3:111849800-111852800	Weak transcription	Pancreas	Pancrea
29	chr3:111849800-111853000	Weak transcription	Small Intestine	intestine
30	chr3:111849800-111853200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:111849800-111853200	Weak transcription	Fetal Heart	heart
32	chr3:111850200-111852600	Weak transcription	Aorta	Aorta
33	chr3:111850800-111852400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr3:111851000-111852400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:111851000-111852400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr3:111851000-111852400	Flanking Active TSS	Fetal Thymus	thymus
37	chr3:111851000-111852600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:111851000-111852600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr3:111851000-111852800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:111851000-111852800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:111851000-111853000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:111851200-111852200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:111851200-111852200	Active TSS	Duodenum Mucosa	Duodenum
44	chr3:111851200-111852400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:111851200-111852600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr3:111851200-111852600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:111851400-111852000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:111851400-111852200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:111851400-111852400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:111851400-111852400	Active TSS	Rectal Mucosa Donor 29	rectum

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