Variant report

Variant	rs4894289
Chromosome Location	chr3:134912008-134912009
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	chr3:134904377..134907908-chr3:134908448..134912165,3	MCF-7	breast:
2	chr3:134908383..134910527-chr3:134911083..134913676,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1027608	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1501195	0.92[EUR][1000 genomes]
rs28594191	0.90[ASN][1000 genomes]
rs35779003	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772636	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4441681	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4569682	0.95[EUR][1000 genomes]
rs4894257	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894258	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894280	0.87[EUR][1000 genomes]
rs4894286	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4894287	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4894290	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439561	0.96[ASN][1000 genomes]
rs6763009	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766459	0.96[ASN][1000 genomes]
rs6776570	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799448	0.92[EUR][1000 genomes]
rs6799471	0.92[EUR][1000 genomes]
rs875368	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs875369	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs882060	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9822213	0.95[EUR][1000 genomes]
rs9824249	0.95[ASN][1000 genomes]
rs9837009	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
2	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:134907200-134913400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:134907400-134922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:134909000-134932400	Weak transcription	Psoas Muscle	Psoas
6	chr3:134909800-134912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:134910000-134913600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:134910000-134914800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:134910000-134926400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:134910200-134923400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:134910800-134932600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:134911000-134922000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:134911400-134912600	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:134911400-134912600	Enhancers	Brain Substantia Nigra	brain
15	chr3:134911400-134912800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:134911400-134913600	Strong transcription	Fetal Brain Female	brain
17	chr3:134911600-134912600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:134911800-134912600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:134912000-134912800	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links