Variant report

Variant	rs1388624
Chromosome Location	chr3:151081412-151081413
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	chr3:151080919..151083079-chr3:151085618..151087424,2	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]
rs10755105	0.85[CEU][hapmap]
rs10935838	0.89[ASN][1000 genomes]
rs11922647	0.85[ASN][1000 genomes]
rs1352887	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs1388619	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388626	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1466684	0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1491978	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491979	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491980	0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1491981	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1873622	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046934	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2172249	0.88[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2870517	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs3732762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732764	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821667	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3971191	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3975401	0.91[ASN][1000 genomes]
rs3975403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3975404	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs4603933	0.84[CHB][hapmap]
rs4679802	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs4680374	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6440731	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6440732	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6763983	0.81[ASN][1000 genomes]
rs6769397	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6782212	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6790748	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs7611328	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7615865	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620353	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7621876	0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7633362	0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9820422	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9877389	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs9878459	0.92[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	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:44 , 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	chr3:151076000-151083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:151078800-151083400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:151079400-151082000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:151079400-151082400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr3:151079400-151082400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:151079800-151082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:151079800-151083000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:151079800-151105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:151080200-151081600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:151080400-151098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:151080400-151101600	Weak transcription	Brain Anterior Caudate	brain
36	chr3:151080400-151105400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:151080600-151081600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:151080800-151085400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:151081000-151082000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:151081000-151088600	Weak transcription	NHDF-Ad	bronchial
41	chr3:151081000-151094600	Weak transcription	Placenta	Placenta
42	chr3:151081200-151081600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:151081400-151082000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:151081400-151085000	Weak transcription	Osteobl	bone

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