Variant report

Variant	rs756212
Chromosome Location	chr5:59069015-59069016
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	JUND	chr5:59068817-59069462	Hela-S3	cervix:	n/a	chr5:59069304-59069315
2	STAT3	chr5:59068611-59069488	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr5:59067905-59069678	Hela-S3	cervix:	n/a	chr5:59068581-59068590
4	STAT3	chr5:59068657-59069458	MCF10A-Er-Src	breast:	n/a	n/a
5	RFX5	chr5:59068684-59069492	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr5:59068590-59069703	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr5:59068999-59069776	MCF-7	breast:	n/a	chr5:59069581-59069588
8	STAT3	chr5:59068734-59069772	MCF10A-Er-Src	breast:	n/a	n/a
9	BRCA1	chr5:59067948-59069744	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:59060717-59070261	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr5:59068658-59069501	MCF10A-Er-Src	breast:	n/a	chr5:59069304-59069315
12	RCOR1	chr5:59068708-59069438	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr5:59068618-59069659	Hela-S3	cervix:	n/a	n/a
14	FOS	chr5:59068653-59069504	MCF10A-Er-Src	breast:	n/a	chr5:59069304-59069315
15	FOS	chr5:59068689-59069504	MCF10A-Er-Src	breast:	n/a	chr5:59069304-59069315
16	MYC	chr5:59068722-59069503	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10043265	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10043283	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs1027747	0.87[YRI][hapmap]
rs10514857	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs11949859	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152908	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12187752	0.83[CHB][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs12188131	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13155799	0.83[CHB][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs1362941	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1362942	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437124	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs1504982	0.93[ASN][1000 genomes]
rs1504984	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16877195	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17310599	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17369708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17381667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs17381695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17381723	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17382202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17440909	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17441217	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17441825	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17742120	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17742544	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17743216	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17799161	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164660	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28583502	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4577665	0.93[ASN][1000 genomes]
rs4699942	0.83[CHB][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs4699943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700341	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs55704150	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55868825	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56199003	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56312915	0.95[EUR][1000 genomes]
rs6450528	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs6450530	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs6860907	0.83[CHB][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs6874708	0.89[ASN][1000 genomes]
rs6889294	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs6897073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751211	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72751218	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72751226	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72751229	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751231	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751232	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751233	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751234	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751235	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751237	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751241	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751244	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751247	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751250	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751252	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72751264	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751266	0.95[EUR][1000 genomes]
rs756211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703963	1.00[JPT][hapmap]
rs7708952	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs7710199	0.89[ASN][1000 genomes]
rs7736817	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs877745	0.83[CHB][hapmap];0.93[ASN][1000 genomes]
rs981230	0.83[CHB][hapmap];0.89[ASN][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	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59065200-59072800	Weak transcription	Aorta	Aorta
2	chr5:59065800-59070000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:59066000-59070400	Enhancers	Hela-S3	cervix
4	chr5:59066000-59081200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59067400-59069200	Enhancers	Colon Smooth Muscle	Colon
6	chr5:59067400-59069400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:59067400-59070000	Enhancers	NHEK	skin
8	chr5:59067600-59070000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr5:59067800-59069200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:59067800-59069400	Enhancers	HMEC	breast
11	chr5:59068000-59069200	Flanking Active TSS	A549	lung
12	chr5:59068200-59085800	Weak transcription	Primary B cells from cord blood	blood
13	chr5:59068800-59069200	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:59069000-59069200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:59069000-59069200	Enhancers	HUES64 Cell Line	embryonic stem cell

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