Variant report

Variant	rs9838371
Chromosome Location	chr3:111482802-111482803
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: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10212300	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10470303	0.96[ASN][1000 genomes]
rs10934106	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10934107	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710738	1.00[ASN][1000 genomes]
rs12490166	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490595	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496925	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496971	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497012	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069980	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074817	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13079085	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4284954	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4431081	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682057	0.95[ASN][1000 genomes]
rs4682305	1.00[ASN][1000 genomes]
rs62273780	1.00[ASN][1000 genomes]
rs6438003	0.87[EUR][1000 genomes]
rs6438008	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438009	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764720	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768713	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777540	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784753	0.97[ASN][1000 genomes]
rs6786386	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786612	0.98[ASN][1000 genomes]
rs6790072	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790079	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792493	0.84[ASN][1000 genomes]
rs6802995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7427201	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609653	0.96[ASN][1000 genomes]
rs7614443	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818574	0.96[ASN][1000 genomes]
rs9823974	0.96[ASN][1000 genomes]
rs9825915	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834030	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863403	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868171	1.00[ASN][1000 genomes]
rs9870823	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	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:54 , 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	chr3:111479800-111483800	Enhancers	A549	lung
7	chr3:111479800-111484400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:111479800-111484800	Enhancers	Osteobl	bone
9	chr3:111480000-111484000	Enhancers	NH-A	brain
10	chr3:111480000-111484400	Enhancers	Colon Smooth Muscle	Colon
11	chr3:111480000-111484400	Enhancers	Hela-S3	cervix
12	chr3:111480200-111484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:111480200-111484400	Enhancers	NHLF	lung
14	chr3:111480200-111484600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:111480200-111492000	Enhancers	Liver	Liver
16	chr3:111480400-111483000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:111480400-111483000	Enhancers	Fetal Stomach	stomach
18	chr3:111480400-111484400	Enhancers	NHEK	skin
19	chr3:111480600-111483000	Weak transcription	Fetal Lung	lung
20	chr3:111480600-111484200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:111480600-111484400	Enhancers	HSMMtube	muscle
22	chr3:111480600-111484800	Enhancers	NHDF-Ad	bronchial
23	chr3:111480600-111486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:111480800-111483400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:111480800-111483400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:111480800-111484200	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:111480800-111484400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:111480800-111484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:111480800-111484400	Enhancers	HSMM	muscle
30	chr3:111480800-111484600	Enhancers	Adipose Nuclei	Adipose
31	chr3:111481000-111483800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:111481000-111487400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:111481000-111487400	Weak transcription	Right Atrium	heart
34	chr3:111481400-111483800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:111481600-111484400	Enhancers	Fetal Intestine Small	intestine
36	chr3:111481800-111484400	Enhancers	Stomach Mucosa	stomach
37	chr3:111481800-111485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:111482000-111483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:111482000-111483800	Weak transcription	Esophagus	oesophagus
40	chr3:111482000-111487400	Weak transcription	Pancreas	Pancrea
41	chr3:111482200-111483400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:111482200-111487200	Weak transcription	Fetal Heart	heart
43	chr3:111482200-111487400	Weak transcription	Left Ventricle	heart
44	chr3:111482600-111483000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:111482600-111484400	Enhancers	Fetal Intestine Large	intestine
46	chr3:111482600-111484400	Enhancers	HepG2	liver
47	chr3:111482600-111487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:111482800-111483000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:111482800-111483200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:111482800-111483200	Enhancers	Sigmoid Colon	Sigmoid Colon

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