Variant report

Variant	rs1375580
Chromosome Location	chr3:145816762-145816763
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	chr3:145808540..145810799-chr3:145816596..145819414,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10935601	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935602	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10935604	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1170390	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11717610	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12492656	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13087364	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13088180	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1375591	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1449443	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1449446	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16857897	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16857919	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982382	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3762694	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792340	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3792345	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804663	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804667	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4611785	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4681293	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4681297	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56686359	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6771106	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771118	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6775684	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6781300	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6783926	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792464	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6794727	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613150	0.90[EUR][1000 genomes]
rs7642940	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9820945	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9836725	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9869137	0.85[AMR][1000 genomes];0.84[EUR][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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
3	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
4	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
5	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
7	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
8	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
14	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
15	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
16	chr3:145794400-145818200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:145794400-145818800	Weak transcription	Ovary	ovary
18	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:145794600-145819200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:145796200-145821400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:145798000-145818400	Weak transcription	HSMMtube	muscle
23	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:145804000-145819200	Weak transcription	NH-A	brain
25	chr3:145804600-145818000	Weak transcription	Fetal Intestine Large	intestine
26	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
27	chr3:145809000-145818200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:145809200-145821600	Weak transcription	HMEC	breast
29	chr3:145809600-145817200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:145810200-145823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:145810400-145817800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:145810400-145829000	Weak transcription	NHLF	lung
33	chr3:145810400-145830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:145810600-145818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:145810600-145827200	Weak transcription	Small Intestine	intestine
37	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:145812000-145818600	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:145812000-145818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:145812000-145826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:145812000-145826800	Weak transcription	Aorta	Aorta
42	chr3:145812200-145817200	Weak transcription	HepG2	liver
43	chr3:145812200-145818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:145812200-145818200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:145812200-145818200	Weak transcription	A549	lung
46	chr3:145812200-145818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:145812200-145818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:145812200-145819400	Weak transcription	Fetal Heart	heart
49	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:145812400-145818000	Weak transcription	Liver	Liver

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