Variant report

Variant	rs6451626
Chromosome Location	chr5:42598607-42598608
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	chr5:42597349..42599170-chr5:43066263..43068120,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177738	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10941578	0.90[JPT][hapmap]
rs11948453	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11949751	1.00[JPT][hapmap]
rs12515372	1.00[AFR][1000 genomes]
rs12520276	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12521020	1.00[JPT][hapmap]
rs13173465	0.86[ASN][1000 genomes]
rs28943879	1.00[AFR][1000 genomes]
rs4075783	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4242115	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4305645	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4314405	0.90[JPT][hapmap];1.00[AFR][1000 genomes]
rs4484445	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4489074	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs4493680	0.90[JPT][hapmap]
rs4504390	1.00[JPT][hapmap]
rs4533898	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4554233	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4866791	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4866936	0.90[JPT][hapmap]
rs6859653	0.90[JPT][hapmap]
rs6887718	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6896667	1.00[JPT][hapmap]
rs7703713	0.90[JPT][hapmap]
rs7721816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7735889	1.00[JPT][hapmap]
rs9968669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42592000-42614400	Weak transcription	Aorta	Aorta
2	chr5:42592200-42600000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:42592200-42605800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:42593000-42601200	Enhancers	Liver	Liver
5	chr5:42595200-42599600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:42595200-42600400	Enhancers	Fetal Heart	heart
7	chr5:42595600-42599000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr5:42596600-42599000	Enhancers	HMEC	breast
9	chr5:42597000-42605600	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:42598000-42598800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:42598000-42598800	Enhancers	NHEK	skin
12	chr5:42598200-42598800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:42598200-42598800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:42598200-42598800	Enhancers	Adipose Nuclei	Adipose
15	chr5:42598200-42599000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:42598400-42599000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:42598400-42600400	Weak transcription	Placenta	Placenta
18	chr5:42598600-42600400	Weak transcription	Psoas Muscle	Psoas
19	chr5:42598600-42603200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:42598600-42603800	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:42598600-42603800	Weak transcription	Left Ventricle	heart
22	chr5:42598600-42604200	Weak transcription	Right Ventricle	heart
23	chr5:42598600-42605800	Weak transcription	Right Atrium	heart

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