Variant report

Variant	rs9882583
Chromosome Location	chr3:145836917-145836918
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145829569..145840903-chr3:145873254..145880972,31	MCF-7	breast:
2	chr3:145834823..145837112-chr3:145844959..145847874,2	MCF-7	breast:
3	chr3:145835695..145838592-chr3:145842329..145844265,2	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	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496198	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496358	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12695808	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063887	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13088158	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349214	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349215	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375581	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375582	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375584	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1375587	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449440	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1449441	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449444	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1449445	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449450	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449451	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512900	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512901	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530741	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1562699	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613698	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613796	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707465	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707466	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707471	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707472	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707473	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707479	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900926	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029137	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029138	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2197908	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305274	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2669396	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864792	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2864793	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35399421	0.89[ASN][1000 genomes]
rs3762691	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792339	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792341	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804660	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804661	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804664	0.86[ASN][1000 genomes]
rs3804665	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804666	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804668	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804669	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804670	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816399	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828381	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681111	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4681112	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4681113	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681294	0.86[ASN][1000 genomes]
rs4681299	0.99[ASN][1000 genomes]
rs6440415	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440417	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440419	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6710	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6783601	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793380	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799720	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800294	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800434	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6801418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802384	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7431590	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7614409	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617913	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7639592	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7641322	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs764755	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs895929	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895930	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289712	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9289713	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289714	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289715	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289716	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289717	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289718	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs959329	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963591	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9809099	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9813047	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822426	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9828112	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842036	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842560	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842865	0.87[AFR][1000 genomes]
rs9852153	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9852725	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9858081	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862005	0.86[ASN][1000 genomes]
rs9862237	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865802	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9874388	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9877411	0.99[ASN][1000 genomes]
rs9878166	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881251	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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
rs9882583	PLOD2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
2	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
4	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:145814200-145841000	Weak transcription	Lung	lung
9	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
10	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
11	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:145824600-145839600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
15	chr3:145827400-145840200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:145827400-145842000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:145828600-145837200	Strong transcription	HSMM	muscle
18	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:145832200-145838400	Weak transcription	Fetal Stomach	stomach
21	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:145833000-145837400	Strong transcription	HUVEC	blood vessel
23	chr3:145833200-145837200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:145833600-145843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:145834200-145837200	Strong transcription	A549	lung
26	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:145834400-145839000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:145834400-145839600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:145834600-145837200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:145834600-145838800	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:145834600-145841200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:145835000-145837200	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr3:145835000-145837600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:145835200-145837000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:145835200-145838400	Weak transcription	Spleen	Spleen
38	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:145835400-145837200	Strong transcription	Fetal Intestine Large	intestine
41	chr3:145835400-145837200	Genic enhancers	Osteobl	bone
42	chr3:145835600-145837000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:145835600-145837400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:145835600-145843600	Weak transcription	NHEK	skin
45	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
46	chr3:145835800-145837200	Strong transcription	Liver	Liver
47	chr3:145835800-145838600	Weak transcription	NH-A	brain
48	chr3:145835800-145843200	Weak transcription	Small Intestine	intestine
49	chr3:145835800-145846000	Weak transcription	Fetal Intestine Small	intestine
50	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas

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