Variant report

Variant	rs57938779
Chromosome Location	chr12:46009229-46009230
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	TCF12	chr12:46008737-46009614	A549	lung:	n/a	chr12:46008742-46008751
2	REST	chr12:46008889-46009414	A549	lung:	n/a	n/a
3	FOXA2	chr12:46008952-46009477	A549	lung:	n/a	n/a
4	CEBPB	chr12:46008921-46009457	MCF-7	breast:	n/a	chr12:46009043-46009056
5	FOS	chr12:46009170-46009485	MCF10A-Er-Src	breast:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
6	HDAC2	chr12:46008959-46009570	MCF-7	breast:	n/a	chr12:46009528-46009542
7	EP300	chr12:46009025-46009338	Hela-S3	cervix:	n/a	chr12:46009237-46009247
8	FOS	chr12:46009160-46009521	Hela-S3	cervix:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
9	TCF12	chr12:46008946-46009645	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:46008976-46009477	HUVEC	blood vessel:	n/a	n/a
11	FOSL2	chr12:46009152-46009585	SK-N-SH	brain:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
12	JUND	chr12:46009010-46009645	SK-N-SH	brain:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
13	GATA3	chr12:46008746-46009710	MCF-7	breast:	n/a	chr12:46009541-46009552 chr12:46008935-46008945 chr12:46009340-46009349
14	GATA3	chr12:46008796-46009466	A549	lung:	n/a	chr12:46008935-46008945 chr12:46009340-46009349
15	EP300	chr12:46008983-46009502	SK-N-SH	brain:	n/a	chr12:46009237-46009247
16	FOXM1	chr12:46009006-46009476	MCF-7	breast:	n/a	n/a
17	ZNF263	chr12:46009103-46009952	HEK293-T-REx	kidney:	n/a	chr12:46009399-46009420
18	CHD2	chr12:46009136-46009483	Hela-S3	cervix:	n/a	n/a
19	FOS	chr12:46009171-46009500	MCF10A-Er-Src	breast:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
20	TCF12	chr12:46008910-46009561	SK-N-SH	brain:	n/a	n/a
21	EP300	chr12:46008914-46009557	MCF-7	breast:	n/a	chr12:46009237-46009247
22	FOXP2	chr12:46009213-46009384	PFSK-1	brain:	n/a	n/a
23	GATA3	chr12:46008815-46009611	MCF-7	breast:	n/a	chr12:46009541-46009552 chr12:46008935-46008945 chr12:46009340-46009349
24	FOSL2	chr12:46009030-46009586	MCF-7	breast:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
25	SP1	chr12:46009009-46009498	A549	lung:	n/a	chr12:46009314-46009328
26	CEBPB	chr12:46009001-46009362	Hela-S3	cervix:	n/a	chr12:46009043-46009056
27	FOS	chr12:46009176-46009494	MCF10A-Er-Src	breast:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
28	REST	chr12:46009182-46009476	PFSK-1	brain:	n/a	n/a
29	RXRA	chr12:46009061-46009486	SK-N-SH	brain:	n/a	n/a
30	STAT3	chr12:46009220-46009380	MCF10A-Er-Src	breast:	n/a	n/a
31	SP1	chr12:46008915-46009492	A549	lung:	n/a	chr12:46009314-46009328
32	KAP1	chr12:46008973-46009767	U2OS	brain:	n/a	n/a
33	EP300	chr12:46009066-46009455	SK-N-SH_RA	brain:	n/a	chr12:46009237-46009247
34	JUND	chr12:46009140-46009493	A549	lung:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
35	FOXA1	chr12:46009167-46009410	T-47D	breast:	n/a	chr12:46009232-46009247
36	GATA3	chr12:46008948-46009548	SK-N-SH	brain:	n/a	chr12:46009340-46009349
37	GATA2	chr12:46009063-46009435	HUVEC	blood vessel:	n/a	chr12:46009340-46009349
38	JUND	chr12:46009055-46009535	SK-N-SH	brain:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
39	JUN	chr12:46009128-46009450	HUVEC	blood vessel:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
40	FOSL2	chr12:46009067-46009540	A549	lung:	n/a	chr12:46009337-46009349 chr12:46009339-46009347
41	FOXA2	chr12:46009105-46009470	A549	lung:	n/a	n/a
42	FOS	chr12:46009163-46009498	MCF10A-Er-Src	breast:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
43	PBX3	chr12:46009068-46009522	SK-N-SH	brain:	n/a	n/a
44	FOXM1	chr12:46008904-46009537	MCF-7	breast:	n/a	n/a
45	GATA3	chr12:46009044-46009538	SK-N-SH	brain:	n/a	chr12:46009340-46009349
46	FOS	chr12:46008935-46009542	HUVEC	blood vessel:	n/a	chr12:46009337-46009349 chr12:46009337-46009348 chr12:46009339-46009347
47	TAF1	chr12:46009100-46009315	PFSK-1	brain:	n/a	n/a
48	EP300	chr12:46008867-46009547	A549	lung:	n/a	chr12:46009237-46009247
49	TFAP2C	chr12:46009140-46009611	Hela-S3	cervix:	n/a	n/a
50	NR2F2	chr12:46008954-46009493	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45989699..45991915-chr12:46007034..46009721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257657	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs34059504	0.95[AFR][1000 genomes]
rs58099600	1.00[AMR][1000 genomes]
rs59132187	0.91[AFR][1000 genomes];1.00[AMR][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	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2751099	chr12:45960118-46043633	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv983462	chr12:46008670-46015543	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46005400-46009400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:46005400-46009400	Weak transcription	NHEK	skin
3	chr12:46005400-46011800	Weak transcription	Right Atrium	heart
4	chr12:46007200-46009800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:46007600-46009600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:46007600-46010600	Enhancers	Hela-S3	cervix
7	chr12:46008200-46009600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:46008200-46009800	Enhancers	Brain Anterior Caudate	brain
9	chr12:46008600-46010000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:46008600-46010000	Enhancers	HUVEC	blood vessel
11	chr12:46008800-46009800	Enhancers	A549	lung
12	chr12:46008800-46010200	Enhancers	NHLF	lung
13	chr12:46009000-46009600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:46009000-46009800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:46009000-46009800	Enhancers	Brain Hippocampus Middle	brain
16	chr12:46009000-46009800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:46009000-46009800	Enhancers	HSMM	muscle
18	chr12:46009000-46009800	Enhancers	NH-A	brain
19	chr12:46009000-46009800	Enhancers	Osteobl	bone
20	chr12:46009000-46010000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:46009000-46010000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:46009000-46010000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:46009000-46010000	Enhancers	Fetal Kidney	kidney
24	chr12:46009000-46010000	Enhancers	HSMMtube	muscle
25	chr12:46009200-46009400	Enhancers	Brain Cingulate Gyrus	brain
26	chr12:46009200-46009600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:46009200-46009600	Enhancers	Brain Angular Gyrus	brain
28	chr12:46009200-46009600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr12:46009200-46009800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:46009200-46009800	Enhancers	Psoas Muscle	Psoas
31	chr12:46009200-46010000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:46009200-46010000	Enhancers	HMEC	breast
33	chr12:46009200-46010000	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links