Variant report

Variant	rs12107581
Chromosome Location	chr3:138093884-138093885
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	chr3:138089900..138093622-chr3:138093776..138096723,3	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002766	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1092338	0.83[ASN][1000 genomes]
rs11710280	0.94[EUR][1000 genomes]
rs11713141	0.83[EUR][1000 genomes]
rs1199330	0.84[ASN][1000 genomes]
rs1199331	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1199337	0.82[ASN][1000 genomes]
rs1199338	0.83[ASN][1000 genomes]
rs12490350	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324341	0.81[ASN][1000 genomes]
rs1564407	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1564408	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678440	0.84[ASN][1000 genomes]
rs1679147	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1720819	0.84[ASN][1000 genomes]
rs185244	0.84[ASN][1000 genomes]
rs1904349	0.80[ASN][1000 genomes]
rs2054468	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061936	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169973	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293252	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35219044	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755751	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773752	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773758	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773759	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816730	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678260	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678261	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678407	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4678408	0.86[EUR][1000 genomes]
rs4678409	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678410	0.90[EUR][1000 genomes]
rs4678411	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4678412	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678415	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678417	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439804	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439805	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6439806	0.93[EUR][1000 genomes]
rs6439807	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67559768	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766859	0.86[EUR][1000 genomes]
rs6769236	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769261	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782181	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782449	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784989	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789235	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6790398	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802211	0.94[EUR][1000 genomes]
rs730158	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731632	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751357	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7615658	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626388	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626424	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637666	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639809	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639850	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642400	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289559	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940233	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825697	0.85[EUR][1000 genomes]
rs9834911	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845672	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846198	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9854465	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9855722	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
2	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
3	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
4	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:138078600-138100600	Weak transcription	NH-A	brain
6	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
7	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:138085800-138096200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:138086200-138100400	Weak transcription	HepG2	liver
14	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:138087000-138096000	Weak transcription	Placenta	Placenta
16	chr3:138087200-138097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
18	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:138087400-138097000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:138087600-138095000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:138089200-138096200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
24	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
27	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:138089600-138100200	Weak transcription	Lung	lung
29	chr3:138090000-138095200	Weak transcription	Brain Germinal Matrix	brain
30	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:138091000-138094600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:138091000-138098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:138091200-138096400	Weak transcription	Brain Anterior Caudate	brain
34	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:138091400-138096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:138091600-138094000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:138091600-138096000	Weak transcription	Right Ventricle	heart
39	chr3:138091600-138098600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:138091800-138094000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:138091800-138094200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:138091800-138098000	Strong transcription	HSMM	muscle
43	chr3:138092000-138094000	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:138092000-138094400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:138092000-138096000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:138092000-138096400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:138092200-138096000	Weak transcription	Fetal Stomach	stomach
48	chr3:138092200-138096800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:138093200-138094000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:138093200-138094600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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