Variant report

Variant	rs58445560
Chromosome Location	chr4:143765580-143765581
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143764792..143768376-chr4:144104488..144107848,3	MCF-7	breast:
2	chr4:143392966..143400087-chr4:143764739..143770446,12	MCF-7	breast:
3	chr4:143391120..143394953-chr4:143764140..143771077,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000250326	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11736709	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939835	0.82[ASN][1000 genomes]
rs13122287	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1441411	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1441417	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1444949	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444950	0.86[AFR][1000 genomes]
rs1992652	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28416530	0.82[ASN][1000 genomes]
rs4690729	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4690730	0.82[ASN][1000 genomes]
rs60263370	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6537129	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6813785	0.82[ASN][1000 genomes]
rs6822703	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823627	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6828896	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6838663	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839158	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6846609	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72728681	0.83[ASN][1000 genomes]
rs72728694	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72728700	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72730409	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72730420	0.80[ASN][1000 genomes]
rs73850583	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7656375	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7663475	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7668263	0.82[ASN][1000 genomes]
rs7685997	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9994364	0.87[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880174	chr4:143639498-143848024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr4:143740200-143765800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143760400-143765800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:143761800-143766200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:143764400-143766800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:143764600-143765600	Active TSS	Fetal Heart	heart
6	chr4:143764800-143765800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr4:143764800-143766200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:143764800-143768800	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:143765000-143765600	Enhancers	A549	lung
10	chr4:143765200-143765600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:143765200-143766600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:143765200-143766800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr4:143765400-143766400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:143765400-143766800	Flanking Active TSS	Dnd41	blood
15	chr4:143765400-143768400	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links