Variant report

Variant	rs17204459
Chromosome Location	chr3:151088098-151088099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151087739..151089244-chr3:151093985..151095599,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10513393	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap]
rs10935846	0.83[LWK][hapmap];0.80[MKK][hapmap]
rs13321176	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs13322120	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327359	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1388625	0.89[CEU][hapmap]
rs17204437	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17282940	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs17282947	0.82[CEU][hapmap]
rs17304673	0.85[CEU][hapmap]
rs6792089	0.82[CEU][hapmap]
rs73008504	1.00[ASN][1000 genomes]
rs73157974	1.00[ASN][1000 genomes]
rs73157994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159921	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73159926	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73159938	0.81[AFR][1000 genomes]
rs7633788	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633828	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634096	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7637803	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9289837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814936	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9817216	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs9819885	0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9821937	0.82[CEU][hapmap]
rs9831242	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs9834154	1.00[ASN][1000 genomes]
rs9838990	0.82[CEU][hapmap]
rs9844557	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848789	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9854017	0.82[CEU][hapmap]
rs9855202	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856118	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9859552	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859854	0.82[CEU][hapmap]
rs9864790	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865547	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867524	1.00[ASN][1000 genomes]
rs9868643	0.81[CEU][hapmap]
rs9868730	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872645	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap]
rs9876268	0.82[CEU][hapmap]
rs9876933	0.82[CEU][hapmap]
rs9881116	1.00[ASW][hapmap];1.00[MEX][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17204459	EVC	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 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	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:151072400-151089800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:151072400-151091400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:151072600-151099800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:151075400-151099800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
12	chr3:151075800-151091200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:151075800-151101200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:151075800-151101400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:151080400-151098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:151080400-151101600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:151081000-151088600	Weak transcription	NHDF-Ad	bronchial
20	chr3:151081000-151094600	Weak transcription	Placenta	Placenta
21	chr3:151082400-151095600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:151083000-151110400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:151083200-151089800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:151084200-151095800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:151084400-151098400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:151084400-151101600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:151084400-151109200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:151084600-151090000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:151085000-151099200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:151085400-151098400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:151085600-151088800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:151085600-151088800	Weak transcription	Osteobl	bone
33	chr3:151086200-151088200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:151086200-151102400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:151087600-151089000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:151087600-151116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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