Variant report

Variant	rs55667430
Chromosome Location	chr13:52785612-52785613
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52768256..52771397-chr13:52784460..52787312,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243406	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1122934	0.87[ASN][1000 genomes]
rs4091568	0.87[ASN][1000 genomes]
rs4941729	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55698745	0.85[AFR][1000 genomes]
rs55715265	0.87[ASN][1000 genomes]
rs57345934	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61957231	0.87[ASN][1000 genomes]
rs61957232	0.87[ASN][1000 genomes]
rs61957233	0.87[ASN][1000 genomes]
rs61957238	0.87[ASN][1000 genomes]
rs61957248	0.87[ASN][1000 genomes]
rs61957249	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61957252	0.87[ASN][1000 genomes]
rs61957253	0.87[ASN][1000 genomes]
rs61957254	0.87[ASN][1000 genomes]
rs61957255	0.87[ASN][1000 genomes]
rs61957256	0.87[ASN][1000 genomes]
rs61957258	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61957297	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61958782	0.87[ASN][1000 genomes]
rs61958784	0.87[ASN][1000 genomes]
rs61958786	0.87[ASN][1000 genomes]
rs61958788	0.87[ASN][1000 genomes]
rs61958800	0.87[ASN][1000 genomes]
rs61958801	0.87[ASN][1000 genomes]
rs61958802	0.87[ASN][1000 genomes]
rs61958803	0.87[ASN][1000 genomes]
rs61958806	0.87[ASN][1000 genomes]
rs61958807	0.87[ASN][1000 genomes]
rs61958860	0.87[ASN][1000 genomes]
rs61958863	0.87[ASN][1000 genomes]
rs61958865	0.87[ASN][1000 genomes]
rs719349	0.87[ASN][1000 genomes]
rs73502305	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73502307	0.87[ASN][1000 genomes]
rs9526818	0.87[ASN][1000 genomes]
rs9526840	0.87[ASN][1000 genomes]
rs9535814	0.87[ASN][1000 genomes]
rs9535818	0.87[ASN][1000 genomes]
rs9535831	0.87[ASN][1000 genomes]
rs9535838	0.87[ASN][1000 genomes]
rs9535839	0.87[ASN][1000 genomes]
rs9535850	0.87[ASN][1000 genomes]
rs9535852	0.87[ASN][1000 genomes]
rs9535859	0.87[ASN][1000 genomes]
rs9535869	0.87[ASN][1000 genomes]
rs9535870	0.87[ASN][1000 genomes]
rs9535875	0.87[ASN][1000 genomes]
rs9535881	0.87[ASN][1000 genomes]
rs9535886	0.87[ASN][1000 genomes]
rs9535890	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535892	0.87[ASN][1000 genomes]
rs9535893	0.87[ASN][1000 genomes]
rs9535894	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535897	0.87[ASN][1000 genomes]
rs9535900	0.87[ASN][1000 genomes]
rs9535901	0.87[ASN][1000 genomes]
rs9535902	0.87[ASN][1000 genomes]
rs9535903	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535906	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535909	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535910	0.87[ASN][1000 genomes]
rs9535911	0.87[ASN][1000 genomes]
rs9535913	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv819887	chr13:52772113-52926921	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv983588	chr13:52772461-52833538	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
9	nsv900083	chr13:52783120-52885838	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52784600-52786200	Enhancers	Placenta	Placenta
2	chr13:52784600-52786400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:52784800-52786000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr13:52785200-52785800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr13:52785200-52786200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:52785200-52786200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:52785400-52785800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:52785400-52786000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:52785600-52786000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:52785600-52786200	Flanking Active TSS	HepG2	liver
11	chr13:52785600-52786200	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links