Variant report

Variant	rs1562699
Chromosome Location	chr3:145847048-145847049
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145845645..145847745-chr3:145881279..145883375,2	MCF-7	breast:
2	chr3:145842696..145844403-chr3:145846645..145849074,2	MCF-7	breast:
3	chr3:145834823..145837112-chr3:145844959..145847874,2	MCF-7	breast:
4	chr3:145843180..145847334-chr3:145876555..145880843,5	MCF-7	breast:
5	chr3:145841131..145847641-chr3:145875218..145882802,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs12171294	1.00[ASN][1000 genomes]
rs12496198	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12496358	0.96[ASN][1000 genomes]
rs12695808	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063887	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13088158	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349214	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349215	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375581	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375582	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375584	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1375587	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449440	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1449441	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449444	0.88[ASN][1000 genomes]
rs1449445	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449450	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449451	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512900	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512901	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530741	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613698	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613796	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707465	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707466	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707471	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707472	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707473	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707479	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900926	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029137	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029138	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2197908	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305274	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2669396	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864792	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2864793	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35399421	0.89[ASN][1000 genomes]
rs3762691	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792339	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792341	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804660	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804661	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804664	0.86[ASN][1000 genomes]
rs3804665	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804666	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804668	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804669	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804670	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816399	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828381	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681111	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4681112	0.87[ASN][1000 genomes]
rs4681113	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681294	0.86[ASN][1000 genomes]
rs4681299	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6440415	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440417	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440419	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6710	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6783601	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793380	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799720	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800294	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800434	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801418	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802384	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7431590	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7614409	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617913	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7639592	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7641322	0.89[ASN][1000 genomes]
rs764755	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs895929	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895930	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289712	0.87[ASN][1000 genomes]
rs9289713	0.93[ASN][1000 genomes]
rs9289714	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289715	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289716	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289717	0.94[ASN][1000 genomes]
rs9289718	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959329	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963591	0.87[ASN][1000 genomes]
rs9809099	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9813047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822426	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9828112	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836521	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842036	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842560	0.99[ASN][1000 genomes]
rs9852153	0.93[ASN][1000 genomes]
rs9852725	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9858081	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858095	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862005	0.86[ASN][1000 genomes]
rs9862237	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865802	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9874388	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9877411	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9878166	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881251	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9882583	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs1562699	PLOD2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
7	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
16	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
17	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:145837200-145851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:145839400-145847600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:145839800-145849000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:145839800-145851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:145840000-145852400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:145840200-145847600	Weak transcription	HSMMtube	muscle
26	chr3:145840200-145849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:145840600-145848600	Weak transcription	Fetal Stomach	stomach
29	chr3:145842000-145849800	Weak transcription	HMEC	breast
30	chr3:145843400-145848800	Weak transcription	Right Atrium	heart
31	chr3:145843400-145851200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:145843600-145848800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:145843600-145848800	Weak transcription	Ovary	ovary
34	chr3:145843600-145855200	Weak transcription	Left Ventricle	heart
35	chr3:145843600-145861200	Weak transcription	Right Ventricle	heart
36	chr3:145844000-145848000	Enhancers	HepG2	liver
37	chr3:145844000-145851200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:145844400-145848800	Weak transcription	NH-A	brain
39	chr3:145844400-145849600	Weak transcription	Fetal Heart	heart
40	chr3:145844600-145848600	Weak transcription	NHLF	lung
41	chr3:145844600-145856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:145844600-145860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:145844800-145847200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:145844800-145848600	Weak transcription	HUVEC	blood vessel
45	chr3:145845000-145848600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:145845000-145848600	Enhancers	Liver	Liver
47	chr3:145845200-145850600	Enhancers	Colon Smooth Muscle	Colon
48	chr3:145845600-145849800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:145845800-145847200	Weak transcription	A549	lung
50	chr3:145846000-145847600	Enhancers	Adipose Nuclei	Adipose

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