Variant report

Variant	rs904593
Chromosome Location	chr3:25193047-25193048
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]
rs2043620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649616	0.85[AFR][1000 genomes]
rs2649619	0.87[AFR][1000 genomes]
rs2885836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321521	0.90[AFR][1000 genomes]
rs321524	0.87[AFR][1000 genomes]
rs321537	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs321540	0.87[AFR][1000 genomes]
rs4258924	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6550953	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793141	0.84[AFR][1000 genomes]
rs6796899	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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:43 , 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	chr3:25191800-25193200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:25191800-25193200	Enhancers	Fetal Muscle Leg	muscle
7	chr3:25191800-25193400	Enhancers	Fetal Stomach	stomach
8	chr3:25192000-25193800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:25192200-25193400	Enhancers	Brain Germinal Matrix	brain
10	chr3:25192200-25193600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:25192400-25194000	Active TSS	Aorta	Aorta
12	chr3:25192600-25193400	Active TSS	Brain Anterior Caudate	brain
13	chr3:25192600-25193400	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr3:25192600-25193600	Active TSS	Colon Smooth Muscle	Colon
15	chr3:25192600-25193600	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:25192600-25194600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:25192800-25193200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:25192800-25193400	Active TSS	Adipose Nuclei	Adipose
19	chr3:25192800-25193400	Enhancers	Fetal Brain Female	brain
20	chr3:25192800-25193400	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:25192800-25193600	Active TSS	Ovary	ovary
22	chr3:25192800-25193800	Active TSS	Right Atrium	heart
23	chr3:25192800-25193800	Flanking Active TSS	HUVEC	blood vessel
24	chr3:25192800-25193800	Active TSS	Osteobl	bone
25	chr3:25192800-25197600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:25192800-25198200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:25192800-25198200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:25193000-25193200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:25193000-25193200	Active TSS	Fetal Brain Male	brain
30	chr3:25193000-25193200	Flanking Active TSS	Fetal Lung	lung
31	chr3:25193000-25193400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr3:25193000-25193400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:25193000-25193400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr3:25193000-25193400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:25193000-25193400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:25193000-25193400	Active TSS	NH-A	brain
37	chr3:25193000-25193600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:25193000-25193600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:25193000-25193600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:25193000-25193600	Active TSS	Fetal Kidney	kidney
41	chr3:25193000-25193600	Active TSS	NHDF-Ad	bronchial
42	chr3:25193000-25193800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:25193000-25193800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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