Variant report

Variant	rs16869742
Chromosome Location	chr5:17375767-17375768
allele	A/C
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	POLR2A	chr5:17375606-17375806	MCF10A-Er-Src	breast:	n/a	n/a
2	TFAP2A	chr5:17375521-17375865	Hela-S3	cervix:	n/a	chr5:17375808-17375817
3	EP300	chr5:17375407-17375933	ECC-1	luminal epithelium:	n/a	chr5:17375832-17375842
4	CEBPB	chr5:17375406-17375892	A549	lung:	n/a	n/a
5	POLR2A	chr5:17375515-17375775	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr5:17375502-17375903	ECC-1	luminal epithelium:	n/a	chr5:17375832-17375842
7	TEAD4	chr5:17375437-17375871	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr5:17375615-17375914	Hela-S3	cervix:	n/a	chr5:17375832-17375842
9	NR3C1	chr5:17375605-17375872	A549	lung:	n/a	chr5:17375808-17375817
10	REST	chr5:17375172-17375988	A549	lung:	n/a	n/a
11	MYC	chr5:17375361-17375959	Hela-S3	cervix:	n/a	n/a
12	FOXA1	chr5:17375612-17375940	ECC-1	luminal epithelium:	n/a	n/a
13	BRCA1	chr5:17375584-17375909	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr5:17375544-17375926	Hela-S3	cervix:	n/a	n/a
15	MAX	chr5:17375261-17375837	A549	lung:	n/a	n/a
16	BACH1	chr5:17375539-17375965	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOXA2	chr5:17375683-17375849	HepG2	liver:	n/a	n/a
18	MAX	chr5:17374917-17376079	A549	lung:	n/a	n/a
19	POLR2A	chr5:17375590-17375817	A549	lung:	n/a	n/a
20	TEAD4	chr5:17375478-17375879	A549	lung:	n/a	n/a
21	FOS	chr5:17375626-17375988	MCF10A-Er-Src	breast:	n/a	chr5:17375808-17375818 chr5:17375808-17375818 chr5:17375807-17375819 chr5:17375808-17375818 chr5:17375809-17375817
22	RAD21	chr5:17375421-17375864	A549	lung:	n/a	n/a
23	FOS	chr5:17375661-17375960	MCF10A-Er-Src	breast:	n/a	chr5:17375808-17375818 chr5:17375808-17375818 chr5:17375807-17375819 chr5:17375808-17375818 chr5:17375809-17375817
24	NR3C1	chr5:17375555-17375929	A549	lung:	n/a	chr5:17375808-17375817
25	SIN3AK20	chr5:17375375-17375925	MCF-7	breast:	n/a	n/a
26	USF1	chr5:17375545-17375858	A549	lung:	n/a	n/a
27	FOSL2	chr5:17375505-17375928	MCF-7	breast:	n/a	chr5:17375808-17375818 chr5:17375808-17375818 chr5:17375807-17375819 chr5:17375808-17375818 chr5:17375809-17375817
28	STAT3	chr5:17375611-17375924	Hela-S3	cervix:	n/a	n/a
29	NR3C1	chr5:17375445-17375978	A549	lung:	n/a	chr5:17375808-17375817
30	YY1	chr5:17375425-17375844	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZNF384	chr5:17375664-17375889	K562	blood:	n/a	n/a
32	EP300	chr5:17375560-17375864	MCF-7	breast:	n/a	chr5:17375832-17375842
33	FOXA1	chr5:17375680-17375936	HepG2	liver:	n/a	n/a
34	CREB1	chr5:17375593-17375827	A549	lung:	n/a	n/a
35	ETS1	chr5:17375472-17375852	A549	lung:	n/a	n/a
36	POLR2A	chr5:17375530-17375808	A549	lung:	n/a	n/a
37	FOXA1	chr5:17375614-17376020	ECC-1	luminal epithelium:	n/a	n/a
38	NR2F2	chr5:17375472-17376038	MCF-7	breast:	n/a	n/a
39	CREB1	chr5:17375487-17375823	A549	lung:	n/a	n/a
40	TFAP2C	chr5:17375496-17375916	Hela-S3	cervix:	n/a	n/a
41	MAX	chr5:17375231-17375939	ECC-1	luminal epithelium:	n/a	n/a
42	CEBPB	chr5:17375567-17375921	Hela-S3	cervix:	n/a	n/a
43	MAX	chr5:17375304-17375935	Hela-S3	cervix:	n/a	n/a
44	NFIC	chr5:17375384-17375939	ECC-1	luminal epithelium:	n/a	n/a
45	SP1	chr5:17375069-17376071	A549	lung:	n/a	n/a
46	USF2	chr5:17375329-17375849	Hela-S3	cervix:	n/a	n/a
47	GATA3	chr5:17375367-17375937	MCF-7	breast:	n/a	n/a
48	NR3C1	chr5:17375569-17375845	ECC-1	luminal epithelium:	n/a	chr5:17375808-17375817
49	ATF3	chr5:17375481-17375880	A549	lung:	n/a	n/a
50	MYC	chr5:17375730-17375792	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:17216760..17218355-chr5:17375692..17378391,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249199	TF binding region
ENSG00000215196	Chromatin interaction
ENSG00000176788	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13153913	0.91[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13173370	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1397576	0.89[CHD][hapmap]
rs1995289	0.84[CHD][hapmap]
rs2459812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34005252	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34060439	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34459662	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34464385	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34668760	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546422	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35568239	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66575349	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71611035	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7707796	0.97[ASN][1000 genomes]
rs7712193	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7731247	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7731729	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732204	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs870893	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs950696	0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv1793466	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	esv1801170	chr5:17364700-17721569	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	esv1820519	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	esv1824831	chr5:17364700-17721569	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	esv1827359	chr5:17364700-17721569	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	esv1828062	chr5:17364700-17721569	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv427713	chr5:17364700-17721569	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv428464	chr5:17364700-17721569	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	esv2757986	chr5:17364700-17936404	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	esv2759328	chr5:17364700-17936404	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv1017469	chr5:17373383-17416643	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16869742	FBXL7	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17371200-17378200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:17371400-17378200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:17373400-17375800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:17373400-17375800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:17373600-17375800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:17373800-17375800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr5:17374200-17375800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:17374400-17378200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:17375000-17375800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:17375000-17375800	Enhancers	Placenta	Placenta
11	chr5:17375000-17375800	Enhancers	HMEC	breast
12	chr5:17375200-17375800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:17375200-17375800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr5:17375200-17375800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:17375200-17375800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:17375200-17375800	Flanking Active TSS	Hela-S3	cervix
17	chr5:17375400-17375800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr5:17375400-17375800	Enhancers	Ovary	ovary
19	chr5:17375400-17375800	Active TSS	A549	lung
20	chr5:17375400-17375800	Flanking Active TSS	NH-A	brain
21	chr5:17375400-17377800	Weak transcription	NHLF	lung
22	chr5:17375600-17375800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr5:17375600-17375800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:17375600-17375800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:17375600-17375800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:17375600-17375800	Enhancers	Lung	lung
27	chr5:17375600-17378000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:17375600-17378400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:17375600-17380800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links