Variant report

Variant	rs28371419
Chromosome Location	chr3:151023230-151023231
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151021234..151025100-chr3:151041293..151045950,7	MCF-7	breast:
2	chr3:151017110..151019943-chr3:151020802..151024030,3	MCF-7	breast:
3	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1048408	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513392	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714714	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719936	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330831	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488267	0.88[ASN][1000 genomes]
rs12494865	0.94[ASN][1000 genomes]
rs1317465	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352886	0.92[ASN][1000 genomes]
rs1472122	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565574	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16863323	0.94[ASN][1000 genomes]
rs16863334	0.94[ASN][1000 genomes]
rs16863336	0.92[ASN][1000 genomes]
rs1844924	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882014	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882015	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882017	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920396	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28497341	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904430	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4475010	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679783	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56105302	0.94[ASN][1000 genomes]
rs56367650	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58334126	0.96[ASN][1000 genomes]
rs62283021	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6765215	0.95[ASN][1000 genomes]
rs6768130	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782313	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6807308	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617677	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7621113	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621183	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621211	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623448	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7653603	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180086	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9757688	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9810067	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827619	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828553	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9829753	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870740	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9875152	0.81[AMR][1000 genomes];0.91[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151021600-151024600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:151021600-151025800	Enhancers	Placenta	Placenta
4	chr3:151021600-151026600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:151021800-151023400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr3:151021800-151023400	Enhancers	HepG2	liver
7	chr3:151021800-151024000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:151021800-151024200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:151021800-151024600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:151021800-151024800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:151022000-151024800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:151022000-151025200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:151022200-151024800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:151022400-151023400	Enhancers	Adipose Nuclei	Adipose
15	chr3:151022400-151023800	Enhancers	Stomach Mucosa	stomach
16	chr3:151022400-151024000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:151022400-151025200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:151022400-151025600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:151022400-151025800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:151022400-151026000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:151022400-151026200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:151022400-151026400	Enhancers	NHLF	lung
23	chr3:151022600-151023400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:151022600-151023400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:151022600-151023400	Flanking Active TSS	A549	lung
26	chr3:151022600-151023800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:151022600-151023800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:151022600-151023800	Enhancers	HSMMtube	muscle
29	chr3:151022600-151024200	Enhancers	HSMM	muscle
30	chr3:151022600-151024400	Flanking Active TSS	Hela-S3	cervix
31	chr3:151022600-151024800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:151022600-151025400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr3:151022600-151026400	Enhancers	NHDF-Ad	bronchial
34	chr3:151022600-151026800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:151022800-151023400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr3:151022800-151023400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:151022800-151023400	Active TSS	HMEC	breast
38	chr3:151022800-151023600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:151022800-151023800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:151022800-151024000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:151022800-151024000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:151022800-151024000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:151023000-151023400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:151023000-151024000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:151023000-151025400	Weak transcription	Esophagus	oesophagus
46	chr3:151023200-151023400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:151023200-151023600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:151023200-151023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:151023200-151023600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:151023200-151023600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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