Variant report

Variant	rs13177853
Chromosome Location	chr5:112632809-112632810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112628459..112631026-chr5:112632248..112634333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10038521	0.86[ASN][1000 genomes]
rs10051115	0.86[ASN][1000 genomes]
rs10053341	0.86[ASN][1000 genomes]
rs10061462	0.86[ASN][1000 genomes]
rs10434754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477490	0.86[ASN][1000 genomes]
rs1157696	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13154300	0.90[ASN][1000 genomes]
rs13159509	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13164135	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171482	0.86[ASN][1000 genomes]
rs13174075	0.86[ASN][1000 genomes]
rs13174151	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13174206	0.90[ASN][1000 genomes]
rs13180516	0.90[ASN][1000 genomes]
rs13180522	0.86[ASN][1000 genomes]
rs13181534	0.86[ASN][1000 genomes]
rs13181732	0.90[ASN][1000 genomes]
rs13181944	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13183383	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13184538	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187823	0.90[ASN][1000 genomes]
rs13189050	0.86[ASN][1000 genomes]
rs13189910	0.86[ASN][1000 genomes]
rs1602862	0.81[ASN][1000 genomes]
rs17325307	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17325503	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17325825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327964	0.90[ASN][1000 genomes]
rs17388260	0.90[ASN][1000 genomes]
rs17389165	0.90[ASN][1000 genomes]
rs1838206	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922678	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1922679	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34316732	0.86[ASN][1000 genomes]
rs34558181	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34682492	0.86[ASN][1000 genomes]
rs34951736	0.90[ASN][1000 genomes]
rs35359071	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35886114	0.86[ASN][1000 genomes]
rs4438866	0.90[ASN][1000 genomes]
rs58268366	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594698	0.93[EUR][1000 genomes]
rs6594706	0.86[ASN][1000 genomes]
rs6594713	0.86[ASN][1000 genomes]
rs6594714	0.86[ASN][1000 genomes]
rs6594715	0.86[ASN][1000 genomes]
rs6594716	0.86[ASN][1000 genomes]
rs66572866	0.90[ASN][1000 genomes]
rs67320720	0.90[ASN][1000 genomes]
rs67693032	0.90[ASN][1000 genomes]
rs6870401	0.86[ASN][1000 genomes]
rs6871934	0.90[ASN][1000 genomes]
rs6872490	0.86[ASN][1000 genomes]
rs6874175	0.90[ASN][1000 genomes]
rs6880562	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6883102	0.88[ASN][1000 genomes]
rs6887482	0.86[ASN][1000 genomes]
rs6887914	0.90[ASN][1000 genomes]
rs6889489	0.86[ASN][1000 genomes]
rs6890874	0.90[ASN][1000 genomes]
rs6896843	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71577442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71577447	0.90[ASN][1000 genomes]
rs71577448	0.90[ASN][1000 genomes]
rs72792189	0.81[ASN][1000 genomes]
rs7701895	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7709646	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7714221	0.86[ASN][1000 genomes]
rs7714760	0.86[ASN][1000 genomes]
rs7717630	0.86[ASN][1000 genomes]
rs7718616	0.90[ASN][1000 genomes]
rs7720414	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725712	0.86[ASN][1000 genomes]
rs7727056	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7727501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729269	0.86[ASN][1000 genomes]
rs7731231	0.86[ASN][1000 genomes]
rs7734576	0.86[ASN][1000 genomes]
rs7737512	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112631200-112633000	Enhancers	HMEC	breast
2	chr5:112631200-112633000	Enhancers	NHEK	skin
3	chr5:112631200-112633200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:112632000-112633000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:112632000-112635600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:112632200-112633000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112632200-112635600	Weak transcription	Ovary	ovary
8	chr5:112632200-112636600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:112632200-112640800	Weak transcription	Right Atrium	heart
10	chr5:112632400-112634000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:112632400-112635600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:112632600-112633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:112632600-112633000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:112632600-112635200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links