Variant report

Variant	rs1707473
Chromosome Location	chr3:145851524-145851525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145851329..145855768-chr3:145877369..145881953,7	MCF-7	breast:
2	chr3:145847747..145850479-chr3:145851136..145852882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs12171294	0.98[ASN][1000 genomes]
rs12496198	0.97[ASN][1000 genomes]
rs12496358	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12695808	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063887	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088158	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1349214	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1349215	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375581	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375582	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1375584	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375587	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449440	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449441	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1449444	0.86[ASN][1000 genomes]
rs1449445	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449450	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449451	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512901	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530741	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562699	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613698	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1613796	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1707465	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707466	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707471	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707472	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707479	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1900926	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029137	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029138	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2197908	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305274	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2669396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864792	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2864793	0.97[ASN][1000 genomes]
rs35399421	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3762691	0.92[ASN][1000 genomes]
rs3792339	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792341	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804660	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804661	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804664	0.84[ASN][1000 genomes]
rs3804665	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804666	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804668	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804669	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804670	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3816399	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828381	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681111	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4681112	0.85[ASN][1000 genomes]
rs4681113	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4681294	0.84[ASN][1000 genomes]
rs4681299	0.97[ASN][1000 genomes]
rs6440415	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6440417	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440419	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6710	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6783601	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793380	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6799720	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800294	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800434	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801418	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802384	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431590	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7614409	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617913	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639592	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7641322	0.91[ASN][1000 genomes]
rs764755	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs895929	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs895930	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289712	0.85[ASN][1000 genomes]
rs9289713	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289714	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289715	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289716	0.92[ASN][1000 genomes]
rs9289717	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289718	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs959329	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963591	0.85[ASN][1000 genomes]
rs9809099	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9813047	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9822426	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828112	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836521	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9842036	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842560	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842865	0.83[AFR][1000 genomes]
rs9852153	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9852725	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858081	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858095	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862005	0.84[ASN][1000 genomes]
rs9862237	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9865802	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874388	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877411	0.97[ASN][1000 genomes]
rs9878166	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881251	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9882583	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	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
2	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
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1707473	PLOD2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
2	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
6	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:145840000-145852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:145843600-145855200	Weak transcription	Left Ventricle	heart
11	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
12	chr3:145844600-145856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:145844600-145860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:145847800-145851600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:145848000-145856800	Weak transcription	Fetal Intestine Small	intestine
16	chr3:145848400-145851600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:145849600-145852400	Enhancers	NHDF-Ad	bronchial
18	chr3:145849600-145852600	Enhancers	HSMMtube	muscle
19	chr3:145849800-145853000	Enhancers	Liver	Liver
20	chr3:145850000-145852200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:145850000-145852800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:145850000-145854400	Enhancers	Osteobl	bone
23	chr3:145850200-145852400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:145850200-145853800	Enhancers	HepG2	liver
25	chr3:145850200-145856200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:145850200-145857600	Weak transcription	NHLF	lung
27	chr3:145850400-145852400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:145850400-145860200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:145850400-145864400	Weak transcription	HMEC	breast
30	chr3:145850600-145851800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:145851000-145851800	Enhancers	HUVEC	blood vessel
32	chr3:145851000-145852000	Enhancers	NH-A	brain
33	chr3:145851000-145853000	Enhancers	Fetal Heart	heart
34	chr3:145851200-145851600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:145851200-145851600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:145851200-145851600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:145851200-145851600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:145851200-145851600	Enhancers	Ovary	ovary
39	chr3:145851200-145851600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr3:145851200-145851600	Enhancers	Right Atrium	heart
41	chr3:145851200-145851600	Enhancers	Small Intestine	intestine
42	chr3:145851200-145851800	Enhancers	Brain Hippocampus Middle	brain
43	chr3:145851200-145851800	Enhancers	Fetal Intestine Large	intestine
44	chr3:145851200-145852600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:145851200-145852600	Enhancers	Fetal Stomach	stomach
46	chr3:145851200-145852800	Enhancers	Adipose Nuclei	Adipose
47	chr3:145851200-145852800	Enhancers	Fetal Lung	lung
48	chr3:145851200-145853000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:145851200-145853000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:145851200-145853000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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