Variant report

Variant	rs62251938
Chromosome Location	chr3:53714500-53714501
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	chr3:53708590..53712002-chr3:53712853..53715298,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12486415	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12492502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872999	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1906537	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2680658	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2680672	0.84[ASN][1000 genomes]
rs34078083	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774515	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55819057	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55948017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6763245	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6765728	0.82[ASN][1000 genomes]
rs6793312	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806330	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs735652	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7648561	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53713200-53716000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53713600-53714600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:53713600-53714600	Enhancers	Fetal Brain Female	brain
5	chr3:53713600-53714600	Enhancers	Fetal Lung	lung
6	chr3:53713600-53715000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:53713800-53714600	Enhancers	Colon Smooth Muscle	Colon
8	chr3:53713800-53714600	Enhancers	Fetal Muscle Leg	muscle
9	chr3:53713800-53714600	Enhancers	Psoas Muscle	Psoas
10	chr3:53713800-53715800	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:53714000-53714600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:53714000-53714600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr3:53714000-53714600	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:53714000-53714600	Enhancers	Brain Substantia Nigra	brain
16	chr3:53714000-53714600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr3:53714000-53714600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr3:53714000-53714600	Enhancers	Left Ventricle	heart
19	chr3:53714000-53714600	Enhancers	Right Atrium	heart
20	chr3:53714000-53714600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:53714000-53715400	Enhancers	Brain Angular Gyrus	brain
22	chr3:53714200-53714600	Enhancers	Ovary	ovary
23	chr3:53714200-53714600	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:53714200-53714800	Enhancers	Fetal Brain Male	brain
25	chr3:53714400-53714600	Bivalent Enhancer	Fetal Stomach	stomach
26	chr3:53714400-53714800	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:53714400-53715200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:53714400-53722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links