Variant report

Variant	rs57902958
Chromosome Location	chr3:111484062-111484063
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	chr3:111482636..111484637-chr3:111486491..111489104,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs13317985	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13321524	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13322494	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13325336	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28479130	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28534728	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28648833	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28675079	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3922706	0.87[ASN][1000 genomes]
rs3922707	0.83[ASN][1000 genomes]
rs3922780	0.87[ASN][1000 genomes]
rs4075549	0.87[ASN][1000 genomes]
rs4276156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4390898	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4516581	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4542994	0.87[ASN][1000 genomes]
rs4634085	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682313	0.87[ASN][1000 genomes]
rs56005252	0.91[ASN][1000 genomes]
rs56052712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56215064	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58124137	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58663746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60867472	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438012	0.87[ASN][1000 genomes]
rs66651424	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66786213	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66856712	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66975684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6762246	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762572	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6778818	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782513	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6787278	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789977	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790355	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790521	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790612	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790825	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790977	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795947	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67970120	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800047	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800065	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802960	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73222475	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73222477	0.91[ASN][1000 genomes]
rs73222500	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7614433	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7627909	0.87[ASN][1000 genomes]
rs9842396	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9843288	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850748	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9858064	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9862472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868898	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871034	0.96[ASN][1000 genomes]
rs9877777	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9880633	0.84[AMR][1000 genomes];0.93[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111477600-111484600	Enhancers	HMEC	breast
2	chr3:111478000-111484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111478800-111484200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:111478800-111484200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:111478800-111484800	Enhancers	Rectal Smooth Muscle	rectum
6	chr3:111479800-111484400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:111479800-111484800	Enhancers	Osteobl	bone
8	chr3:111480000-111484400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:111480000-111484400	Enhancers	Hela-S3	cervix
10	chr3:111480200-111484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:111480200-111484400	Enhancers	NHLF	lung
12	chr3:111480200-111484600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:111480200-111492000	Enhancers	Liver	Liver
14	chr3:111480400-111484400	Enhancers	NHEK	skin
15	chr3:111480600-111484200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:111480600-111484400	Enhancers	HSMMtube	muscle
17	chr3:111480600-111484800	Enhancers	NHDF-Ad	bronchial
18	chr3:111480600-111486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:111480800-111484200	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:111480800-111484400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:111480800-111484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:111480800-111484400	Enhancers	HSMM	muscle
23	chr3:111480800-111484600	Enhancers	Adipose Nuclei	Adipose
24	chr3:111481000-111487400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:111481000-111487400	Weak transcription	Right Atrium	heart
26	chr3:111481600-111484400	Enhancers	Fetal Intestine Small	intestine
27	chr3:111481800-111484400	Enhancers	Stomach Mucosa	stomach
28	chr3:111481800-111485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:111482000-111487400	Weak transcription	Pancreas	Pancrea
30	chr3:111482200-111487200	Weak transcription	Fetal Heart	heart
31	chr3:111482200-111487400	Weak transcription	Left Ventricle	heart
32	chr3:111482600-111484400	Enhancers	Fetal Intestine Large	intestine
33	chr3:111482600-111484400	Enhancers	HepG2	liver
34	chr3:111482600-111487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:111482800-111484600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:111482800-111487200	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:111482800-111487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:111483000-111484200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:111483000-111487400	Weak transcription	Fetal Stomach	stomach
40	chr3:111483200-111484200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:111483200-111487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:111483200-111489200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:111483400-111484200	Enhancers	Placenta	Placenta
44	chr3:111483400-111484600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:111483400-111487200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:111483400-111487400	Weak transcription	Fetal Lung	lung
47	chr3:111483800-111484200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:111483800-111484400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:111483800-111484600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:111483800-111484600	Flanking Active TSS	A549	lung

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