Variant report

Variant	rs7642699
Chromosome Location	chr3:89041352-89041353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12486137	0.80[AFR][1000 genomes]
rs12495112	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566054	0.80[AFR][1000 genomes]
rs2132581	0.80[AFR][1000 genomes]
rs2132585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677013	0.82[ASN][1000 genomes]
rs33923135	0.80[AFR][1000 genomes]
rs34372398	0.81[AFR][1000 genomes]
rs4105153	0.80[AFR][1000 genomes]
rs56870794	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62276534	0.80[AFR][1000 genomes]
rs62276535	0.80[AFR][1000 genomes]
rs6793785	0.80[AFR][1000 genomes]
rs6803153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619269	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7636945	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641434	0.80[AFR][1000 genomes]
rs7643738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310101	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825143	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9830451	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs9849740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853326	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9882138	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv834759	chr3:88901229-89105366	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1002060	chr3:88984502-89047104	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv536637	chr3:88984502-89047104	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877158	chr3:89018866-89103302	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv525314	chr3:89031440-89051475	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89040200-89042000	Enhancers	HMEC	breast
2	chr3:89040200-89042000	Enhancers	NHEK	skin
3	chr3:89040400-89041800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:89040400-89042000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:89040400-89042000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:89041000-89041400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:89041200-89041400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:89041200-89042600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:89041200-89045800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links