Variant report

Variant	rs17080872
Chromosome Location	chr3:47485029-47485030
allele	C/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	FOXA1	chr3:47484461-47485579	HepG2	liver:	n/a	n/a
2	FOSL2	chr3:47484771-47485526	HepG2	liver:	n/a	chr3:47485321-47485332
3	FOXA1	chr3:47484503-47485558	HepG2	liver:	n/a	n/a
4	BRCA1	chr3:47484711-47485105	HepG2	liver:	n/a	n/a
5	BCL3	chr3:47484786-47485633	A549	lung:	n/a	n/a
6	NFIC	chr3:47484637-47485134	HepG2	liver:	n/a	n/a
7	MXI1	chr3:47484379-47485559	HepG2	liver:	n/a	n/a
8	MYBL2	chr3:47484468-47485675	HepG2	liver:	n/a	n/a
9	HEY1	chr3:47484492-47485614	HepG2	liver:	n/a	n/a
10	EP300	chr3:47484540-47485494	HepG2	liver:	n/a	chr3:47484638-47484654
11	SRF	chr3:47484510-47485107	ECC-1	luminal epithelium:	n/a	chr3:47484822-47484840 chr3:47484822-47484840
12	JUND	chr3:47484551-47485538	HepG2	liver:	n/a	chr3:47485321-47485332
13	CEBPB	chr3:47484654-47485042	ECC-1	luminal epithelium:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
14	FOS	chr3:47484638-47485957	MCF10A-Er-Src	breast:	n/a	chr3:47485321-47485332
15	SMC3	chr3:47484590-47485525	HepG2	liver:	n/a	n/a
16	MAX	chr3:47484745-47485030	Hela-S3	cervix:	n/a	chr3:47484949-47484959
17	EP300	chr3:47484576-47485589	HepG2	liver:	n/a	chr3:47485513-47485527 chr3:47484638-47484654
18	RAD21	chr3:47484645-47485464	HepG2	liver:	n/a	chr3:47485334-47485347
19	FOS	chr3:47484659-47485457	MCF10A-Er-Src	breast:	n/a	chr3:47485321-47485332
20	MAX	chr3:47484569-47485462	HepG2	liver:	n/a	chr3:47484949-47484959
21	CEBPB	chr3:47484560-47485030	MCF-7	breast:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
22	MYC	chr3:47484627-47485944	MCF10A-Er-Src	breast:	n/a	chr3:47484949-47484959
23	CEBPB	chr3:47484649-47485174	IMR90	lung:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
24	JUND	chr3:47484410-47485506	HepG2	liver:	n/a	chr3:47485321-47485332
25	CEBPB	chr3:47484594-47485046	MCF-7	breast:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
26	TBP	chr3:47484562-47485430	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:47484462-47485427	HepG2	liver:	n/a	n/a
28	CEBPB	chr3:47484642-47485433	HepG2	liver:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
29	JUN	chr3:47484718-47485161	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:47484472-47485411	HepG2	liver:	n/a	n/a
31	FOSL2	chr3:47484801-47485564	A549	lung:	n/a	chr3:47485321-47485332
32	FOSL2	chr3:47484573-47485529	HepG2	liver:	n/a	chr3:47485321-47485332
33	HNF4A	chr3:47484591-47485537	HepG2	liver:	n/a	chr3:47485377-47485392 chr3:47485378-47485391 chr3:47485379-47485391 chr3:47485377-47485392 chr3:47485378-47485392 chr3:47485376-47485384 chr3:47485377-47485392 chr3:47485377-47485392 chr3:47485378-47485390 chr3:47485378-47485386 chr3:47485379-47485391
34	POLR2A	chr3:47484710-47485376	MCF10A-Er-Src	breast:	n/a	n/a
35	NR2F2	chr3:47484497-47485623	HepG2	liver:	n/a	n/a
36	SRF	chr3:47484545-47485069	ECC-1	luminal epithelium:	n/a	chr3:47484822-47484840 chr3:47484822-47484840
37	MAFK	chr3:47484649-47485621	HepG2	liver:	n/a	n/a
38	SP1	chr3:47484439-47485540	HepG2	liver:	n/a	chr3:47484950-47484964
39	ZNF217	chr3:47484679-47485061	MCF-7	breast:	n/a	n/a
40	MAZ	chr3:47484504-47485475	HepG2	liver:	n/a	chr3:47484949-47484959
41	FOS	chr3:47484674-47485917	MCF10A-Er-Src	breast:	n/a	chr3:47485321-47485332
42	RXRA	chr3:47484521-47485509	HepG2	liver:	n/a	n/a
43	FOXA2	chr3:47484525-47485144	HepG2	liver:	n/a	n/a
44	FOS	chr3:47484627-47485951	MCF10A-Er-Src	breast:	n/a	chr3:47485321-47485332
45	MAZ	chr3:47484239-47485721	IMR90	lung:	n/a	chr3:47484340-47484349 chr3:47484949-47484959
46	TEAD4	chr3:47484419-47485564	HepG2	liver:	n/a	n/a
47	MYC	chr3:47484627-47486015	MCF10A-Er-Src	breast:	n/a	chr3:47484949-47484959
48	ARID3A	chr3:47484405-47485577	HepG2	liver:	n/a	n/a
49	CEBPB	chr3:47484694-47485034	A549	lung:	n/a	chr3:47484828-47484839 chr3:47484829-47484840
50	BHLHE40	chr3:47484473-47485547	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47484894..47485414-chr3:47514547..47515158,2	MCF-7	breast:
2	chr3:47479631..47481186-chr3:47484843..47486561,2	MCF-7	breast:

Variant related genes	Relation type
SCAP	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038394	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs10490798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs1076394	0.81[JPT][hapmap]
rs10865946	0.87[CHB][hapmap]
rs11130123	0.81[JPT][hapmap]
rs11130124	0.81[JPT][hapmap]
rs11130128	0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11130129	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11705957	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs11710013	0.81[JPT][hapmap]
rs11710322	0.81[JPT][hapmap]
rs11711824	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs11716763	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs11719877	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs12490383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12495169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12636851	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs13059519	0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs13075233	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs1531875	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs1638676	0.81[JPT][hapmap]
rs17411375	0.81[JPT][hapmap]
rs1872164	0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2101247	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2240796	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs295428	0.81[JPT][hapmap]
rs295441	0.81[JPT][hapmap]
rs295442	0.81[JPT][hapmap]
rs295458	0.81[JPT][hapmap]
rs3816779	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs4858811	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4858868	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs4858893	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4858894	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs60369822	0.80[ASN][1000 genomes]
rs6792461	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs6800271	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs7649234	0.81[ASN][1000 genomes]
rs7651762	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs807932	0.81[JPT][hapmap]
rs807936	0.81[JPT][hapmap]
rs811115	0.86[JPT][hapmap]
rs878659	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs922957	0.87[CHB][hapmap]
rs9683033	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9683177	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv511233	chr3:47484797-47494157	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17080872	CCDC12	cis	parietal	SCAN
rs17080872	CCDC12	cis	cerebellum	SCAN
rs17080872	CELSR3	cis	cerebellum	SCAN
rs17080872	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs17080872	SCAP	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:47472400-47485200	Weak transcription	Fetal Brain Male	brain
3	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
4	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47476000-47485800	Weak transcription	Fetal Kidney	kidney
6	chr3:47476600-47485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:47479600-47485800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:47480400-47485200	Strong transcription	K562	blood
10	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47481600-47486000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:47481800-47492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:47482200-47488800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:47482600-47486400	Enhancers	Stomach Mucosa	stomach
16	chr3:47483000-47486000	Enhancers	Fetal Intestine Large	intestine
17	chr3:47483000-47486400	Enhancers	Fetal Intestine Small	intestine
18	chr3:47483200-47487400	Enhancers	Liver	Liver
19	chr3:47483400-47486000	Enhancers	Pancreas	Pancrea
20	chr3:47483400-47486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:47483600-47485200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:47483600-47485800	Enhancers	Fetal Heart	heart
23	chr3:47483600-47486000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:47483800-47485200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:47483800-47485400	Enhancers	Ovary	ovary
26	chr3:47483800-47485600	Enhancers	Esophagus	oesophagus
27	chr3:47483800-47486000	Enhancers	Psoas Muscle	Psoas
28	chr3:47483800-47486000	Enhancers	Right Ventricle	heart
29	chr3:47484000-47485200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:47484000-47486200	Enhancers	Brain Hippocampus Middle	brain
31	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
32	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:47484200-47485400	Enhancers	Gastric	stomach
34	chr3:47484200-47485400	Enhancers	Right Atrium	heart
35	chr3:47484200-47485400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr3:47484200-47485400	Enhancers	Spleen	Spleen
37	chr3:47484200-47485600	Enhancers	Brain Angular Gyrus	brain
38	chr3:47484200-47485800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:47484200-47486000	Enhancers	Adipose Nuclei	Adipose
40	chr3:47484200-47486000	Enhancers	Colonic Mucosa	Colon
41	chr3:47484200-47486000	Enhancers	Small Intestine	intestine
42	chr3:47484200-47486200	Enhancers	Placenta	Placenta
43	chr3:47484200-47486200	Enhancers	NHLF	lung
44	chr3:47484200-47486600	Enhancers	Fetal Muscle Leg	muscle
45	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:47484400-47485200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:47484400-47485200	Weak transcription	Brain Germinal Matrix	brain
48	chr3:47484400-47485200	Enhancers	Rectal Smooth Muscle	rectum
49	chr3:47484400-47485400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:47484400-47485400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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