Variant report

Variant	rs11718741
Chromosome Location	chr3:145872063-145872064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145870477..145872332-chr3:145872492..145874567,2	MCF-7	breast:
2	chr3:145868830..145872262-chr3:145881585..145883218,3	MCF-7	breast:
3	chr3:145865509..145867074-chr3:145870719..145872599,2	K562	blood:
4	chr3:145864521..145866275-chr3:145870715..145872248,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10935601	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10935605	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935608	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1170389	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1170390	0.83[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1170391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1170392	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1170393	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927021	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12498084	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13087364	0.84[JPT][hapmap]
rs13088646	0.89[JPT][hapmap]
rs1375588	0.86[EUR][1000 genomes]
rs1375591	0.83[JPT][hapmap]
rs1707468	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1707469	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17413767	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17414130	0.80[JPT][hapmap]
rs1868541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1913186	0.94[JPT][hapmap]
rs1982382	0.82[JPT][hapmap]
rs2137485	0.85[ASN][1000 genomes]
rs34800183	0.83[ASN][1000 genomes]
rs4681297	0.83[JPT][hapmap]
rs4681301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56842856	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57327675	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57945878	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60267871	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60811409	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61050446	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61154334	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766101	0.80[JPT][hapmap]
rs6781300	0.83[JPT][hapmap]
rs6783926	0.80[JPT][hapmap]
rs6792464	0.83[JPT][hapmap]
rs71304237	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73148985	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73148986	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73148991	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613150	0.83[JPT][hapmap]
rs7623263	0.89[JPT][hapmap]
rs7642940	0.84[JPT][hapmap]
rs965032	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9820945	0.83[JPT][hapmap]
rs9836725	0.84[JPT][hapmap]
rs9869137	0.86[JPT][hapmap]

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
rs11718741	PLOD2	Cis_1M	lymphoblastoid	RTeQTL
rs11718741	PLOD2	cis	Muscle Skeletal	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	chr3:145861800-145872200	Weak transcription	Adipose Nuclei	Adipose
10	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
12	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:145862000-145873800	Weak transcription	NHLF	lung
15	chr3:145862400-145874000	Weak transcription	Lung	lung
16	chr3:145864400-145872200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:145864400-145873000	Genic enhancers	Osteobl	bone
18	chr3:145866800-145873600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:145866800-145873800	Weak transcription	NHDF-Ad	bronchial
20	chr3:145867000-145873600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:145867000-145873800	Weak transcription	Fetal Lung	lung
22	chr3:145868000-145874000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:145870000-145874000	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:145870200-145873000	Enhancers	Fetal Heart	heart
25	chr3:145870200-145873800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:145870400-145872600	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr3:145870600-145876800	Weak transcription	Hela-S3	cervix
28	chr3:145870800-145876800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:145871000-145873600	Weak transcription	Brain Anterior Caudate	brain
30	chr3:145871000-145874000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:145871000-145874000	Enhancers	Fetal Intestine Small	intestine
32	chr3:145871000-145874000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:145871000-145874000	Weak transcription	Stomach Mucosa	stomach
34	chr3:145871200-145873800	Weak transcription	HMEC	breast
35	chr3:145871400-145872200	Enhancers	Colon Smooth Muscle	Colon
36	chr3:145871400-145872800	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr3:145871400-145873800	Enhancers	Liver	Liver
38	chr3:145871400-145873800	Weak transcription	Brain Substantia Nigra	brain
39	chr3:145871400-145873800	Weak transcription	NH-A	brain
40	chr3:145871400-145874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:145871400-145874000	Weak transcription	Fetal Stomach	stomach
42	chr3:145871400-145874000	Weak transcription	Right Ventricle	heart
43	chr3:145871400-145877800	Weak transcription	Gastric	stomach
44	chr3:145871600-145872600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:145871600-145872600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:145871600-145872800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:145871600-145873200	Weak transcription	Left Ventricle	heart
48	chr3:145871600-145873600	Weak transcription	Aorta	Aorta
49	chr3:145871600-145873600	Weak transcription	Right Atrium	heart
50	chr3:145871600-145873600	Enhancers	Stomach Smooth Muscle	stomach

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