Variant report

Variant	rs9878860
Chromosome Location	chr3:159542576-159542577
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	BCL3	chr3:159542047-159542654	A549	lung:	n/a	n/a
2	FOSL2	chr3:159542025-159542613	SK-N-SH	brain:	n/a	chr3:159542245-159542253
3	JUND	chr3:159541895-159542608	SK-N-SH	brain:	n/a	chr3:159542245-159542253
4	TCF12	chr3:159541780-159542649	SK-N-SH	brain:	n/a	chr3:159541825-159541834
5	NR2F2	chr3:159542048-159542661	MCF-7	breast:	n/a	n/a
6	RCOR1	chr3:159541795-159542733	IMR90	lung:	n/a	n/a
7	PBX3	chr3:159541863-159542655	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr3:159541978-159542582	MCF-7	breast:	n/a	n/a
9	TCF12	chr3:159541891-159542581	ECC-1	luminal epithelium:	n/a	n/a
10	GATA3	chr3:159541870-159542749	MCF-7	breast:	n/a	n/a
11	GATA3	chr3:159541872-159542597	SK-N-SH	brain:	n/a	n/a
12	CEBPB	chr3:159541908-159542583	MCF-7	breast:	n/a	n/a
13	PBX3	chr3:159541965-159542606	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr3:159541936-159542629	SK-N-SH	brain:	n/a	n/a
15	EP300	chr3:159541971-159542590	ECC-1	luminal epithelium:	n/a	n/a
16	JUND	chr3:159541940-159542602	SK-N-SH	brain:	n/a	chr3:159542245-159542253
17	TCF12	chr3:159541859-159542681	SK-N-SH	brain:	n/a	n/a
18	JUND	chr3:159541911-159542622	MCF-7	breast:	n/a	chr3:159542245-159542253
19	REST	chr3:159542181-159542611	MCF-7	breast:	n/a	n/a
20	NR3C1	chr3:159542041-159542606	A549	lung:	n/a	chr3:159542347-159542354 chr3:159542359-159542380
21	FOXA1	chr3:159541977-159542613	A549	lung:	n/a	n/a
22	STAT3	chr3:159542064-159542650	MCF10A-Er-Src	breast:	n/a	n/a
23	EP300	chr3:159541966-159542597	SK-N-SH	brain:	n/a	n/a
24	RXRA	chr3:159541940-159542644	SK-N-SH	brain:	n/a	n/a
25	NFIC	chr3:159541851-159542576	ECC-1	luminal epithelium:	n/a	n/a
26	TCF12	chr3:159541819-159542660	A549	lung:	n/a	chr3:159541825-159541834
27	NFIC	chr3:159542013-159542629	SK-N-SH	brain:	n/a	n/a
28	STAT3	chr3:159541989-159542597	Hela-S3	cervix:	n/a	n/a
29	SP1	chr3:159541870-159542603	A549	lung:	n/a	n/a
30	FOSL2	chr3:159541882-159542653	A549	lung:	n/a	chr3:159542245-159542253
31	ATF3	chr3:159541970-159542601	A549	lung:	n/a	n/a
32	GATA3	chr3:159541783-159542663	A549	lung:	n/a	n/a
33	NR3C1	chr3:159541994-159542589	ECC-1	luminal epithelium:	n/a	chr3:159542347-159542354 chr3:159542359-159542380

Variant related genes	Relation type
ENSG00000264146	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10440023	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470474	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470475	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513545	0.82[MKK][hapmap];1.00[TSI][hapmap]
rs13314923	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28493475	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs28695486	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4621369	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56786891	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781743	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015941	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015943	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015951	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015956	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015967	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017937	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017960	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612849	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615917	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7651449	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9290049	0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs9811600	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814058	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9816506	1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9820062	0.83[AMR][1000 genomes]
rs9821194	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9830331	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845205	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845849	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846391	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846673	0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs9846819	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850723	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851155	0.83[AMR][1000 genomes]
rs9853947	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853973	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854679	0.85[AMR][1000 genomes]
rs9855171	1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861347	0.90[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs9865889	0.85[AMR][1000 genomes]
rs9872127	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877761	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9880866	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159532400-159546400	Weak transcription	Fetal Stomach	stomach
2	chr3:159536400-159543200	Weak transcription	Esophagus	oesophagus
3	chr3:159536600-159543000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:159536600-159543000	Weak transcription	Pancreas	Pancrea
5	chr3:159536600-159543200	Weak transcription	Colonic Mucosa	Colon
6	chr3:159536600-159546400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:159537000-159543000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:159537000-159543000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:159537000-159543000	Weak transcription	Lung	lung
10	chr3:159537000-159546400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:159537000-159546600	Weak transcription	Right Atrium	heart
12	chr3:159537600-159544000	Enhancers	HMEC	breast
13	chr3:159537600-159544200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:159537800-159543000	Weak transcription	Right Ventricle	heart
15	chr3:159537800-159543000	Weak transcription	Spleen	Spleen
16	chr3:159538000-159543800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:159538400-159543800	Enhancers	NHDF-Ad	bronchial
18	chr3:159540400-159544400	Enhancers	Stomach Smooth Muscle	stomach
19	chr3:159540600-159542800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:159540600-159543200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:159540600-159543800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:159540600-159543800	Enhancers	Colon Smooth Muscle	Colon
23	chr3:159540600-159543800	Enhancers	NHLF	lung
24	chr3:159540800-159543400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:159540800-159543800	Enhancers	NHEK	skin
26	chr3:159540800-159544000	Enhancers	HSMMtube	muscle
27	chr3:159540800-159546400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:159541200-159542800	Enhancers	HUVEC	blood vessel
29	chr3:159541200-159543400	Enhancers	Hela-S3	cervix
30	chr3:159541200-159543400	Enhancers	NH-A	brain
31	chr3:159541200-159543400	Enhancers	Osteobl	bone
32	chr3:159541200-159543800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:159541200-159543800	Enhancers	Fetal Intestine Large	intestine
34	chr3:159541400-159543400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:159541400-159543400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:159541400-159543400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:159541400-159543800	Enhancers	Brain Hippocampus Middle	brain
38	chr3:159541400-159543800	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:159541400-159546400	Weak transcription	Psoas Muscle	Psoas
40	chr3:159541600-159542600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:159541600-159543000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:159541600-159543000	Weak transcription	Left Ventricle	heart
43	chr3:159541600-159543000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:159541600-159543800	Enhancers	Fetal Heart	heart
45	chr3:159541800-159542800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:159541800-159543000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:159541800-159543800	Enhancers	Fetal Kidney	kidney
48	chr3:159542000-159542600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:159542000-159543000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:159542000-159543800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links