Variant report

Variant	rs1388625
Chromosome Location	chr3:151080416-151080417
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	chr3:151074684..151076586-chr3:151078527..151080909,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10513393	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321176	0.94[CEU][hapmap]
rs13322120	0.89[CEU][hapmap]
rs13327359	0.88[CEU][hapmap]
rs17204437	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17204459	0.89[CEU][hapmap]
rs17282940	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17282947	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17304673	0.93[CEU][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28386791	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28734805	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55751359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780660	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6792089	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73157938	0.86[EUR][1000 genomes]
rs73157954	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73157974	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73157991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7633788	0.89[CEU][hapmap]
rs7633828	0.89[CEU][hapmap]
rs7634096	0.89[CEU][hapmap]
rs7637803	0.89[CEU][hapmap]
rs9289837	0.89[CEU][hapmap]
rs9812617	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814936	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9817216	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs9819885	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9821749	0.80[EUR][1000 genomes]
rs9821937	0.94[CEU][hapmap]
rs9831242	0.94[CEU][hapmap]
rs9834154	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9836053	0.83[CEU][hapmap]
rs9838990	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9840232	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9841430	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9844557	0.88[CEU][hapmap]
rs9848789	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9854017	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs9855202	0.89[CEU][hapmap]
rs9856118	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9859552	0.89[CEU][hapmap]
rs9859854	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9867524	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9868643	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9871624	0.84[CEU][hapmap]
rs9872645	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9875587	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9876268	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9876933	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880395	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9881116	0.89[CEU][hapmap]

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	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151063800-151099800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:151064400-151089200	Weak transcription	NHLF	lung
3	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:151065600-151109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:151065800-151082200	Weak transcription	Fetal Thymus	thymus
7	chr3:151067800-151083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:151068000-151082600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:151070400-151082800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:151072400-151089800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:151072400-151091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:151074200-151082800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:151074200-151083800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:151074200-151084000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:151075200-151082800	Weak transcription	Pancreas	Pancrea
18	chr3:151075200-151084000	Weak transcription	Gastric	stomach
19	chr3:151075400-151099800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
21	chr3:151075800-151084600	Weak transcription	Dnd41	blood
22	chr3:151075800-151091200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:151075800-151101200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:151075800-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:151076000-151081000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:151076000-151083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:151077200-151081200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:151078800-151083400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:151079400-151082000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:151079400-151082400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:151079400-151082400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:151079600-151081400	Enhancers	Adipose Nuclei	Adipose
33	chr3:151079800-151080600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:151079800-151081000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:151079800-151082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:151079800-151083000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:151080000-151081000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:151080200-151080600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:151080200-151081000	Enhancers	NHDF-Ad	bronchial
41	chr3:151080200-151081600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:151080400-151080800	Weak transcription	Placenta	Placenta
43	chr3:151080400-151081400	Enhancers	Osteobl	bone
44	chr3:151080400-151098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:151080400-151101600	Weak transcription	Brain Anterior Caudate	brain
46	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle

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