Variant report

Variant	rs1515577
Chromosome Location	chr3:120128940-120128941
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	chr3:120127740..120129651-chr3:120130782..120132515,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1056928	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057231	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147693	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147694	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147696	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1147698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259328	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061630	1.00[JPT][hapmap]
rs13081675	1.00[JPT][hapmap]
rs13081694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13096256	1.00[JPT][hapmap]
rs13097755	1.00[JPT][hapmap]
rs13100865	1.00[JPT][hapmap]
rs13709	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs1492272	1.00[JPT][hapmap]
rs17813772	1.00[JPT][hapmap]
rs1969356	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091726	1.00[JPT][hapmap]
rs2272515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676698	1.00[JPT][hapmap]
rs4676776	1.00[JPT][hapmap]
rs4676778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676781	1.00[JPT][hapmap]
rs4676782	1.00[JPT][hapmap]
rs4676783	1.00[JPT][hapmap]
rs6438575	1.00[JPT][hapmap]
rs869247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880550	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120112000-120132600	Strong transcription	Placenta Amnion	Placenta Amnion
2	chr3:120112200-120130000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr3:120112200-120131400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:120112200-120132600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:120112400-120129600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr3:120112400-120130200	Strong transcription	Adipose Nuclei	Adipose
7	chr3:120112400-120132600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:120112400-120132600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:120112400-120132600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:120112400-120132600	Strong transcription	HSMMtube	muscle
11	chr3:120112400-120132600	Strong transcription	NH-A	brain
12	chr3:120112400-120132600	Strong transcription	NHDF-Ad	bronchial
13	chr3:120112400-120132600	Strong transcription	NHLF	lung
14	chr3:120112600-120130600	Strong transcription	Ovary	ovary
15	chr3:120112600-120131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:120112600-120132400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:120112600-120132400	Strong transcription	Aorta	Aorta
18	chr3:120112600-120132600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:120112600-120132600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:120112600-120132800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:120112800-120131200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:120112800-120132000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:120112800-120132600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:120112800-120132600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:120113200-120132400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:120113200-120132600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:120113200-120132600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:120113200-120132600	Strong transcription	Fetal Kidney	kidney
29	chr3:120113200-120132600	Strong transcription	HUVEC	blood vessel
30	chr3:120113200-120133000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:120113400-120132400	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr3:120113400-120132600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr3:120113400-120132600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:120113800-120132600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:120114000-120132400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:120114200-120129600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:120114400-120132600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:120114400-120132800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
40	chr3:120114800-120129200	Strong transcription	Colon Smooth Muscle	Colon
41	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:120118800-120135600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:120122200-120136000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:120122400-120135000	Weak transcription	Psoas Muscle	Psoas
45	chr3:120122400-120135800	Weak transcription	A549	lung
46	chr3:120123400-120129200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr3:120123400-120131400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:120123400-120131600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:120123600-120131200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:120124000-120129200	Strong transcription	Colonic Mucosa	Colon

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