Variant report

Variant	rs12471986
Chromosome Location	chr2:179146883-179146884
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	STAT3	chr2:179146761-179147172	MCF10A-Er-Src	breast:	n/a	n/a
2	NR3C1	chr2:179146752-179147088	A549	lung:	n/a	n/a
3	TEAD4	chr2:179146743-179147271	K562	blood:	n/a	n/a
4	CEBPB	chr2:179146757-179147071	A549	lung:	n/a	n/a
5	STAT3	chr2:179146847-179147229	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:179146770-179147198	PFSK-1	brain:	n/a	n/a
7	FOS	chr2:179146840-179147116	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr2:179146804-179147167	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr2:179146795-179147083	IMR90	lung:	n/a	n/a
10	POLR2A	chr2:179146802-179147283	MCF10A-Er-Src	breast:	n/a	n/a
11	SP1	chr2:179146707-179147226	A549	lung:	n/a	chr2:179147018-179147032 chr2:179147073-179147086
12	FOXA1	chr2:179146863-179147049	T-47D	breast:	n/a	n/a
13	FOXA2	chr2:179146758-179147169	A549	lung:	n/a	n/a
14	E2F4	chr2:179146865-179147126	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr2:179146780-179147175	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA2	chr2:179146792-179147121	A549	lung:	n/a	n/a
17	FOS	chr2:179146868-179147128	MCF10A-Er-Src	breast:	n/a	n/a
18	RCOR1	chr2:179146814-179147212	K562	blood:	n/a	n/a
19	CEBPB	chr2:179146795-179147086	K562	blood:	n/a	n/a
20	ELF1	chr2:179146720-179147089	K562	blood:	n/a	chr2:179146924-179146937
21	NFIC	chr2:179146719-179147338	SK-N-SH	brain:	n/a	chr2:179146971-179146988
22	FOS	chr2:179146804-179147171	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr2:179146814-179147175	MCF10A-Er-Src	breast:	n/a	n/a
24	EP300	chr2:179146866-179147014	K562	blood:	n/a	n/a
25	TBL1XR1	chr2:179146870-179147070	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179140423..179143363-chr2:179145106..179148015,2	K562	blood:
2	chr2:179058189..179060134-chr2:179145387..179147817,2	MCF-7	breast:

Variant related genes	Relation type
OSBPL6	TF binding region
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10167889	0.86[EUR][1000 genomes]
rs12467696	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13401080	1.00[ASN][1000 genomes]
rs13402976	0.84[MEX][hapmap]
rs1368903	1.00[CHB][hapmap]
rs1368907	1.00[CHB][hapmap]
rs1434081	1.00[CHB][hapmap]
rs16866260	1.00[CHB][hapmap]
rs16866274	1.00[CHB][hapmap]
rs16866276	1.00[CHB][hapmap]
rs1992753	0.86[EUR][1000 genomes]
rs333988	0.86[EUR][1000 genomes]
rs334595	1.00[CHB][hapmap]
rs334596	1.00[CHB][hapmap]
rs334597	1.00[CHB][hapmap]
rs334601	1.00[CHB][hapmap]
rs334603	0.84[MEX][hapmap]
rs334607	1.00[CHB][hapmap]
rs334609	1.00[CHB][hapmap]
rs334611	0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs334613	0.80[EUR][1000 genomes]
rs4894005	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894006	0.85[EUR][1000 genomes]
rs4894007	1.00[CHB][hapmap]
rs4894013	0.84[MEX][hapmap]
rs62177256	0.84[EUR][1000 genomes]
rs62177257	0.86[EUR][1000 genomes]
rs62179160	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179161	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179162	0.87[EUR][1000 genomes]
rs62179163	0.85[EUR][1000 genomes]
rs62179164	0.85[EUR][1000 genomes]
rs62179165	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179167	0.83[EUR][1000 genomes]
rs6433718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433719	1.00[CHB][hapmap]
rs6725937	1.00[CHB][hapmap]
rs6743122	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756568	1.00[ASN][1000 genomes]
rs6760059	0.83[MEX][hapmap]
rs7585689	1.00[CHB][hapmap]
rs9808049	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12471986	ATP5G3	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179143000-179160200	Weak transcription	Fetal Kidney	kidney
2	chr2:179143200-179160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:179144000-179148400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:179144200-179163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:179144400-179153000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:179144400-179154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:179144600-179147000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:179144600-179147000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:179144600-179149400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:179144600-179149600	Weak transcription	HSMMtube	muscle
12	chr2:179144600-179155000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:179145000-179159200	Weak transcription	Liver	Liver
14	chr2:179146000-179149800	Enhancers	Fetal Intestine Small	intestine
15	chr2:179146400-179150000	Enhancers	Fetal Intestine Large	intestine
16	chr2:179146600-179147200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:179146600-179147200	Flanking Active TSS	A549	lung
18	chr2:179146600-179147200	Enhancers	Hela-S3	cervix
19	chr2:179146600-179147200	Enhancers	Osteobl	bone
20	chr2:179146600-179147400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:179146600-179147400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:179146600-179147400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:179146600-179147400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr2:179146600-179147400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:179146600-179147400	Enhancers	HMEC	breast
26	chr2:179146600-179147400	Enhancers	HUVEC	blood vessel
27	chr2:179146600-179147400	Enhancers	K562	blood
28	chr2:179146600-179147400	Enhancers	NH-A	brain
29	chr2:179146600-179147400	Enhancers	NHEK	skin
30	chr2:179146600-179147800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:179146600-179147800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:179146600-179147800	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr2:179146600-179148000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:179146600-179151600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:179146800-179147000	Enhancers	Brain Angular Gyrus	brain
36	chr2:179146800-179147200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:179146800-179147200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:179146800-179147200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:179146800-179147200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:179146800-179147200	Enhancers	Esophagus	oesophagus
41	chr2:179146800-179147200	Enhancers	Fetal Lung	lung
42	chr2:179146800-179147200	Enhancers	Psoas Muscle	Psoas
43	chr2:179146800-179147200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr2:179146800-179147200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr2:179146800-179147400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:179146800-179147400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr2:179146800-179147400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:179146800-179147400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:179146800-179147400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:179146800-179147400	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links