Variant report

Variant	rs1239949
Chromosome Location	chr13:51106369-51106370
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	chr13:51106080-51106400	MCF10A-Er-Src	breast:	n/a	n/a
2	RAD21	chr13:51106034-51106464	H1-hESC	embryonic stem cell:	n/a	chr13:51106230-51106249
3	RAD21	chr13:51106053-51106414	GM12878	blood:	n/a	chr13:51106230-51106249
4	CTCF	chr13:51106077-51106389	A549	lung:	n/a	chr13:51106232-51106250
5	CTCF	chr13:51105797-51106573	A549	lung:	n/a	chr13:51106232-51106250
6	RAD21	chr13:51106020-51106472	SK-N-SH_RA	brain:	n/a	chr13:51106230-51106249
7	RAD21	chr13:51105942-51106504	HCT-116	colon:	n/a	chr13:51106230-51106249
8	RAD21	chr13:51105947-51106498	IMR90	lung:	n/a	chr13:51106230-51106249
9	RAD21	chr13:51106069-51106428	H1-hESC	embryonic stem cell:	n/a	chr13:51106230-51106249
10	FOS	chr13:51105998-51106383	MCF10A-Er-Src	breast:	n/a	n/a
11	RAD21	chr13:51106107-51106446	A549	lung:	n/a	chr13:51106230-51106249
12	CTCF	chr13:51106110-51106393	K562	blood:	n/a	chr13:51106232-51106250
13	RAD21	chr13:51106007-51106457	SK-N-SH_RA	brain:	n/a	chr13:51106230-51106249
14	SMC3	chr13:51105605-51107176	SK-N-SH	brain:	n/a	chr13:51106234-51106248
15	CTCF	chr13:51106010-51106394	HepG2	liver:	n/a	chr13:51106232-51106250
16	RAD21	chr13:51106112-51106381	GM12878	blood:	n/a	chr13:51106230-51106249
17	RAD21	chr13:51106035-51106427	H1-hESC	embryonic stem cell:	n/a	chr13:51106230-51106249
18	RAD21	chr13:51105925-51106519	HCT-116	colon:	n/a	chr13:51106230-51106249
19	ARID3A	chr13:51106167-51106391	HepG2	liver:	n/a	n/a
20	CTCF	chr13:51106107-51106378	Spleen_OC	spleen:	n/a	chr13:51106232-51106250
21	CTCF	chr13:51106095-51106385	HUVEC	blood vessel:	n/a	chr13:51106232-51106250
22	RAD21	chr13:51105971-51106505	MCF-7	breast:	n/a	chr13:51106230-51106249
23	SMC3	chr13:51105995-51106447	Hela-S3	cervix:	n/a	chr13:51106234-51106248
24	CTCF	chr13:51105734-51106467	SK-N-SH	brain:	n/a	chr13:51106232-51106250
25	RAD21	chr13:51105994-51106508	MCF-7	breast:	n/a	chr13:51106230-51106249
26	CTCF	chr13:51106280-51106430	WI-38	lung:	n/a	n/a
27	RAD21	chr13:51105884-51106529	HepG2	liver:	n/a	chr13:51106230-51106249
28	CTCF	chr13:51106220-51106370	GM12865	blood:	n/a	chr13:51106232-51106250
29	SMC3	chr13:51106031-51106469	GM12878	blood:	n/a	chr13:51106234-51106248
30	RAD21	chr13:51105970-51106431	HepG2	liver:	n/a	chr13:51106230-51106249
31	RAD21	chr13:51105973-51106448	Hela-S3	cervix:	n/a	chr13:51106230-51106249
32	CTCF	chr13:51106146-51106371	Medullo	brain:	n/a	chr13:51106232-51106250
33	CTCF	chr13:51106018-51106420	MCF-7	breast:	n/a	chr13:51106232-51106250
34	RAD21	chr13:51106108-51106380	HepG2	liver:	n/a	chr13:51106230-51106249
35	CTCF	chr13:51106011-51106485	IMR90	lung:	n/a	chr13:51106232-51106250
36	CTCF	chr13:51106000-51106471	MCF-7	breast:	n/a	chr13:51106232-51106250
37	RAD21	chr13:51105725-51106784	SK-N-SH	brain:	n/a	chr13:51106230-51106249
38	CTCF	chr13:51106220-51106370	HCT-116	colon:	n/a	chr13:51106232-51106250
39	CTCF	chr13:51105922-51106487	HCT-116	colon:	n/a	chr13:51106232-51106250
40	CTCF	chr13:51106034-51106445	GM12878	blood:	n/a	chr13:51106232-51106250
41	CTCF	chr13:51106240-51106390	A549	lung:	n/a	n/a
42	FOS	chr13:51105993-51106385	MCF10A-Er-Src	breast:	n/a	n/a
43	RAD21	chr13:51105930-51106522	A549	lung:	n/a	chr13:51106230-51106249
44	CTCF	chr13:51106220-51106370	HVMF	connective:	n/a	chr13:51106232-51106250
45	RAD21	chr13:51106034-51106460	A549	lung:	n/a	chr13:51106230-51106249
46	SMC3	chr13:51106089-51106423	HepG2	liver:	n/a	chr13:51106234-51106248
47	RAD21	chr13:51106006-51106423	GM12878	blood:	n/a	chr13:51106230-51106249
48	RAD21	chr13:51105915-51106484	ECC-1	luminal epithelium:	n/a	chr13:51106230-51106249

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:60083238..60083858-chr13:51105851..51106693,2	MCF-7	breast:
2	chr13:50698162..50700615-chr13:51105796..51107576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229323	TF binding region
ENSG00000231607	Chromatin interaction

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

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

rs_ID	r²[population]
rs1239955	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs149870	0.84[YRI][hapmap]
rs671786	0.85[YRI][hapmap];1.00[AFR][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51103800-51110600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51104000-51106400	Weak transcription	Thymus	Thymus
3	chr13:51104000-51106800	Enhancers	Osteobl	bone
4	chr13:51104400-51106800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:51104600-51106600	Weak transcription	HMEC	breast
6	chr13:51104600-51106600	Weak transcription	HUVEC	blood vessel
7	chr13:51104600-51107000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:51104800-51108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:51104800-51110600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:51105600-51107000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:51105800-51107200	Enhancers	NH-A	brain
12	chr13:51106000-51107800	Weak transcription	Dnd41	blood
13	chr13:51106200-51106400	Enhancers	Adipose Nuclei	Adipose
14	chr13:51106200-51106400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr13:51106200-51108400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:51106200-51110600	Weak transcription	HSMM	muscle

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