Variant report

Variant	rs6793380
Chromosome Location	chr3:145873068-145873069
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	chr3:145870477..145872332-chr3:145872492..145874567,2	MCF-7	breast:
2	chr3:145872676..145874418-chr3:145880885..145882915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs12171294	0.86[ASN][1000 genomes]
rs12496198	0.86[ASN][1000 genomes]
rs12496358	0.82[ASN][1000 genomes]
rs12695808	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13063887	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1349214	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1349215	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1355685	0.82[ASN][1000 genomes]
rs1375582	0.82[EUR][1000 genomes]
rs1375584	0.82[EUR][1000 genomes]
rs1375587	0.81[EUR][1000 genomes]
rs1449440	0.86[EUR][1000 genomes]
rs1449450	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449451	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1512900	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1512901	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530741	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1562699	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1613698	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1613796	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1707465	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1707466	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1707471	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1707472	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1707473	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1707479	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1900926	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029137	0.82[EUR][1000 genomes]
rs2029138	0.82[EUR][1000 genomes]
rs2197908	0.82[EUR][1000 genomes]
rs2305274	0.81[EUR][1000 genomes]
rs2669396	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864792	0.86[EUR][1000 genomes]
rs2864793	0.86[ASN][1000 genomes]
rs35399421	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762691	0.81[ASN][1000 genomes]
rs3792339	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792341	0.82[EUR][1000 genomes]
rs3804660	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804661	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3804670	0.81[EUR][1000 genomes]
rs3816399	0.91[EUR][1000 genomes]
rs3828381	0.82[EUR][1000 genomes]
rs4681111	0.82[EUR][1000 genomes]
rs4681113	0.81[EUR][1000 genomes]
rs4681299	0.86[ASN][1000 genomes]
rs6440415	0.81[EUR][1000 genomes]
rs6440417	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440419	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710	0.81[EUR][1000 genomes]
rs6783601	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799720	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6800294	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6800434	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6801418	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6802384	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7614409	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617913	0.82[EUR][1000 genomes]
rs7639592	0.82[EUR][1000 genomes]
rs7641322	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7645622	0.85[ASN][1000 genomes]
rs764755	0.82[EUR][1000 genomes]
rs895929	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs895930	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289714	0.87[EUR][1000 genomes]
rs9289715	0.87[EUR][1000 genomes]
rs9289716	0.81[ASN][1000 genomes]
rs9289717	0.81[ASN][1000 genomes]
rs9289718	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs959329	0.81[EUR][1000 genomes]
rs9809099	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813047	0.82[EUR][1000 genomes]
rs9822426	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9828112	0.87[EUR][1000 genomes]
rs9836521	0.90[EUR][1000 genomes]
rs9842036	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9842560	0.86[ASN][1000 genomes]
rs9852725	0.82[EUR][1000 genomes]
rs9858081	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858095	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862237	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9865802	0.87[EUR][1000 genomes]
rs9874388	0.82[EUR][1000 genomes]
rs9877411	0.86[ASN][1000 genomes]
rs9878166	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9881251	0.86[EUR][1000 genomes]
rs9882583	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6793380	PLOD2	cis	Esophagus Mucosa	GTEx
rs6793380	PLOD2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
2	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:145860800-145874000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
11	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:145862000-145873800	Weak transcription	NHLF	lung
14	chr3:145862400-145874000	Weak transcription	Lung	lung
15	chr3:145866800-145873600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:145866800-145873800	Weak transcription	NHDF-Ad	bronchial
17	chr3:145867000-145873600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:145867000-145873800	Weak transcription	Fetal Lung	lung
19	chr3:145868000-145874000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:145870000-145874000	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:145870200-145873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:145870600-145876800	Weak transcription	Hela-S3	cervix
23	chr3:145870800-145876800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:145871000-145873600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:145871000-145874000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:145871000-145874000	Enhancers	Fetal Intestine Small	intestine
27	chr3:145871000-145874000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:145871000-145874000	Weak transcription	Stomach Mucosa	stomach
29	chr3:145871200-145873800	Weak transcription	HMEC	breast
30	chr3:145871400-145873800	Enhancers	Liver	Liver
31	chr3:145871400-145873800	Weak transcription	Brain Substantia Nigra	brain
32	chr3:145871400-145873800	Weak transcription	NH-A	brain
33	chr3:145871400-145874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:145871400-145874000	Weak transcription	Fetal Stomach	stomach
35	chr3:145871400-145874000	Weak transcription	Right Ventricle	heart
36	chr3:145871400-145877800	Weak transcription	Gastric	stomach
37	chr3:145871600-145873200	Weak transcription	Left Ventricle	heart
38	chr3:145871600-145873600	Weak transcription	Aorta	Aorta
39	chr3:145871600-145873600	Weak transcription	Right Atrium	heart
40	chr3:145871600-145873600	Enhancers	Stomach Smooth Muscle	stomach
41	chr3:145871600-145873600	Weak transcription	HSMM	muscle
42	chr3:145871600-145873800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:145871600-145873800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:145871600-145873800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:145871600-145873800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:145871600-145873800	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:145871600-145873800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:145871600-145873800	Weak transcription	Fetal Kidney	kidney
49	chr3:145871600-145873800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:145871600-145873800	Enhancers	HepG2	liver

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