Variant report

Variant	rs57945878
Chromosome Location	chr3:145874219-145874220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145804083..145806262-chr3:145874178..145876137,2	MCF-7	breast:
2	chr3:145870477..145872332-chr3:145872492..145874567,2	MCF-7	breast:
3	chr3:145872676..145874418-chr3:145880885..145882915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10935605	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935606	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935608	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1170389	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1170391	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1170392	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1170393	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718741	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927021	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12498084	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1375588	0.84[EUR][1000 genomes]
rs1707468	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1707469	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17413767	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868541	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2137485	0.84[ASN][1000 genomes]
rs34800183	0.82[ASN][1000 genomes]
rs4681301	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56842856	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57327675	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60267871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60811409	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61050446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61154334	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71304237	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73148985	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73148986	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73148991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965032	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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
rs57945878	PLOD2	Cis_1M	lymphoblastoid	RTeQTL
rs57945878	PLOD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:145870600-145876800	Weak transcription	Hela-S3	cervix
5	chr3:145870800-145876800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:145871400-145877800	Weak transcription	Gastric	stomach
7	chr3:145871600-145874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:145871600-145874400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:145871600-145876800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:145871600-145877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:145871600-145877600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:145871800-145876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:145872800-145875800	Enhancers	Fetal Intestine Large	intestine
14	chr3:145873000-145875800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:145873000-145877600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:145873400-145874400	Enhancers	Fetal Heart	heart
17	chr3:145873600-145874400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:145873600-145874400	Active TSS	Right Atrium	heart
19	chr3:145873600-145874400	Flanking Active TSS	Osteobl	bone
20	chr3:145873600-145875200	Flanking Active TSS	A549	lung
21	chr3:145873600-145875800	Active TSS	Aorta	Aorta
22	chr3:145873600-145876600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:145873600-145879800	Active TSS	Stomach Smooth Muscle	stomach
24	chr3:145873800-145874400	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:145873800-145874400	Active TSS	NHLF	lung
26	chr3:145873800-145874600	Flanking Active TSS	HSMM	muscle
27	chr3:145873800-145874800	Flanking Active TSS	Liver	Liver
28	chr3:145873800-145874800	Flanking Active TSS	NHDF-Ad	bronchial
29	chr3:145873800-145875000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:145873800-145875000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:145873800-145875000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:145873800-145875000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr3:145873800-145875000	Enhancers	Brain Substantia Nigra	brain
34	chr3:145873800-145875000	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr3:145873800-145875000	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr3:145873800-145875600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:145873800-145875600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:145873800-145875600	Enhancers	Fetal Kidney	kidney
39	chr3:145873800-145876000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:145873800-145876000	Enhancers	NH-A	brain
41	chr3:145873800-145876200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:145873800-145876800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:145873800-145876800	Enhancers	Fetal Lung	lung
44	chr3:145873800-145877000	Flanking Active TSS	HUVEC	blood vessel
45	chr3:145874000-145874400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:145874000-145874400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:145874000-145874400	Active TSS	Ovary	ovary
48	chr3:145874000-145874400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:145874000-145874400	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:145874000-145874400	Active TSS	HepG2	liver

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