Variant report

Variant	rs12054346
Chromosome Location	chr3:69164993-69164994
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69158126..69159711-chr3:69164338..69166265,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1051901	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1131960	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[EUR][1000 genomes]
rs17005366	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];1.00[EUR][1000 genomes]
rs3772980	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772983	1.00[EUR][1000 genomes]
rs3796213	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3796214	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[EUR][1000 genomes]
rs3821564	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56152276	1.00[EUR][1000 genomes]
rs56194306	1.00[EUR][1000 genomes]
rs56280964	1.00[EUR][1000 genomes]
rs57159802	1.00[EUR][1000 genomes]
rs58277851	1.00[EUR][1000 genomes]
rs59090383	1.00[EUR][1000 genomes]
rs60230066	0.99[ASN][1000 genomes]
rs60474520	1.00[EUR][1000 genomes]
rs72924853	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72924854	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73835722	1.00[EUR][1000 genomes]
rs73835726	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73835727	1.00[EUR][1000 genomes]
rs73835728	1.00[EUR][1000 genomes]
rs73835729	1.00[EUR][1000 genomes]
rs7617775	0.86[EUR][1000 genomes]
rs7621394	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621929	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629932	0.96[ASN][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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv2762334	chr3:69157085-69173375	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69153800-69165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:69153800-69168000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:69154000-69165000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:69154000-69165800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:69154000-69167800	Weak transcription	Pancreas	Pancrea
6	chr3:69154000-69170200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:69154400-69166000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:69155400-69165800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:69155800-69165400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:69155800-69166200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:69155800-69170200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:69158400-69167200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:69160400-69165800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:69160600-69172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:69163200-69166800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:69163200-69170000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:69163400-69165000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:69163400-69165400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:69163600-69166000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:69163600-69171600	Weak transcription	Fetal Lung	lung
21	chr3:69163800-69165400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:69164000-69165800	Weak transcription	Psoas Muscle	Psoas
23	chr3:69164200-69166400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:69164400-69167400	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr3:69164600-69165400	Weak transcription	Left Ventricle	heart
26	chr3:69164600-69166000	Enhancers	Brain Hippocampus Middle	brain
27	chr3:69164600-69166000	Active TSS	HSMMtube	muscle
28	chr3:69164600-69166200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr3:69164600-69166600	Enhancers	HMEC	breast
30	chr3:69164600-69167400	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr3:69164800-69165000	Flanking Active TSS	Fetal Heart	heart
32	chr3:69164800-69165400	Enhancers	NH-A	brain
33	chr3:69164800-69165600	Enhancers	NHDF-Ad	bronchial
34	chr3:69164800-69165600	Enhancers	NHLF	lung
35	chr3:69164800-69165600	Enhancers	Osteobl	bone
36	chr3:69164800-69166000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:69164800-69166000	Active TSS	Right Ventricle	heart
38	chr3:69164800-69166200	Active TSS	Fetal Muscle Leg	muscle
39	chr3:69164800-69166200	Enhancers	HSMM	muscle
40	chr3:69164800-69166400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:69164800-69166400	Enhancers	Brain Substantia Nigra	brain
42	chr3:69164800-69166600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:69164800-69166600	Active TSS	Right Atrium	heart
44	chr3:69164800-69166600	Enhancers	NHEK	skin

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