Variant report

Variant	rs11927021
Chromosome Location	chr3:145877400-145877401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145787365..145792721-chr3:145875341..145880381,7	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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935608	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1170389	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1170391	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1170392	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1170393	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11718741	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12498084	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375588	0.84[EUR][1000 genomes]
rs1707468	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1707469	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17413767	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868541	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137485	0.86[ASN][1000 genomes]
rs34800183	0.84[ASN][1000 genomes]
rs4681301	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56842856	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57327675	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57945878	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60267871	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60811409	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61050446	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61154334	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71304237	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73148985	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73148986	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73148991	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs965032	0.96[EUR][1000 genomes];0.84[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
rs11927021	PLOD2	cis	Muscle Skeletal	GTEx
rs11927021	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145871400-145877800	Weak transcription	Gastric	stomach
2	chr3:145871600-145877600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:145873000-145877600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:145873600-145879800	Active TSS	Stomach Smooth Muscle	stomach
5	chr3:145874000-145877800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:145874200-145878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:145874200-145880000	Active TSS	Right Ventricle	heart
8	chr3:145874600-145877800	Weak transcription	Pancreas	Pancrea
9	chr3:145874600-145878000	Weak transcription	Lung	lung
10	chr3:145874600-145878000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:145874800-145877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:145874800-145877800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:145874800-145878000	Weak transcription	Stomach Mucosa	stomach
14	chr3:145874800-145880000	Active TSS	Ovary	ovary
15	chr3:145874800-145880000	Active TSS	Right Atrium	heart
16	chr3:145874800-145880600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:145875000-145877400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:145875000-145877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:145875000-145877600	Weak transcription	Psoas Muscle	Psoas
20	chr3:145875000-145878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:145875000-145880400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:145875600-145880000	Active TSS	A549	lung
23	chr3:145875800-145877400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:145876000-145877400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:145876000-145878200	Weak transcription	Spleen	Spleen
26	chr3:145876000-145879600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:145876000-145879800	Active TSS	Colon Smooth Muscle	Colon
28	chr3:145876000-145879800	Active TSS	HSMMtube	muscle
29	chr3:145876000-145880000	Active TSS	Aorta	Aorta
30	chr3:145876200-145879800	Active TSS	Fetal Kidney	kidney
31	chr3:145876200-145879800	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:145876400-145878600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:145876400-145879600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:145876400-145879800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:145876600-145877800	Weak transcription	Small Intestine	intestine
36	chr3:145876600-145878000	Active TSS	Brain Anterior Caudate	brain
37	chr3:145876600-145879600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr3:145876600-145879600	Active TSS	NHLF	lung
39	chr3:145876600-145879800	Active TSS	Placenta Amnion	Placenta Amnion
40	chr3:145876600-145880000	Active TSS	Fetal Stomach	stomach
41	chr3:145876800-145877400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:145876800-145877400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr3:145876800-145877400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:145876800-145877400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:145876800-145877400	Enhancers	Hela-S3	cervix
46	chr3:145876800-145877800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:145876800-145879200	Active TSS	Brain Hippocampus Middle	brain
48	chr3:145876800-145879600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:145876800-145879600	Active TSS	Fetal Intestine Large	intestine
50	chr3:145876800-145879600	Bivalent/Poised TSS	HepG2	liver

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