Variant report

Variant	rs2043620
Chromosome Location	chr3:25194091-25194092
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	chr3:25187342..25189876-chr3:25191897..25194177,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2043619	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2363595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649616	0.82[AFR][1000 genomes]
rs2649619	0.85[AFR][1000 genomes]
rs2885836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321521	0.88[AFR][1000 genomes]
rs321524	0.85[AFR][1000 genomes]
rs321537	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs321540	0.84[AFR][1000 genomes]
rs4258924	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6550953	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793141	0.83[AFR][1000 genomes]
rs6796899	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs904593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978142	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][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	nsv1013446	chr3:25176609-25221334	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876631	chr3:25185448-25231571	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25190600-25194400	Weak transcription	Fetal Heart	heart
2	chr3:25191000-25194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:25191400-25194600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:25191400-25195200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:25192600-25194600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:25192800-25197600	Weak transcription	Brain Angular Gyrus	brain
7	chr3:25192800-25198200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:25192800-25198200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:25193200-25194600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:25193200-25196200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:25193400-25194400	Weak transcription	Fetal Lung	lung
12	chr3:25193400-25194600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:25193400-25194600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:25193400-25194600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:25193400-25194800	Enhancers	Fetal Brain Male	brain
16	chr3:25193400-25197200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:25193400-25197200	Weak transcription	NH-A	brain
18	chr3:25193400-25197600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:25193400-25197800	Weak transcription	Fetal Stomach	stomach
20	chr3:25193400-25197800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:25193600-25194600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:25193600-25197000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:25193600-25197200	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:25193600-25197400	Weak transcription	NHDF-Ad	bronchial
25	chr3:25193600-25197600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:25193800-25194600	Weak transcription	Right Atrium	heart
27	chr3:25193800-25194800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:25193800-25195000	Enhancers	HUVEC	blood vessel
29	chr3:25193800-25196800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:25193800-25197200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:25193800-25197400	Weak transcription	Osteobl	bone
32	chr3:25194000-25197400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:25194000-25197600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:25194000-25197600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:25194000-25211800	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links