Variant report

Variant	rs60811409
Chromosome Location	chr3:145867364-145867365
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145863564..145865449-chr3:145867210..145869807,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10935605	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935606	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935608	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1170389	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1170390	0.85[AFR][1000 genomes]
rs1170391	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1170392	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1170393	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718741	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927021	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12498084	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1375588	0.83[EUR][1000 genomes]
rs1707468	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707469	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17413767	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868541	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2137485	0.83[ASN][1000 genomes]
rs34800183	0.81[ASN][1000 genomes]
rs4681301	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56842856	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57327675	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57945878	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60267871	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61050446	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61154334	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71304237	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148985	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73148986	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73148991	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965032	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60811409	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
3	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:145860600-145868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:145860800-145870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:145860800-145874000	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:145861000-145869000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:145861000-145870200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:145861400-145870200	Weak transcription	Small Intestine	intestine
15	chr3:145861400-145870600	Weak transcription	NH-A	brain
16	chr3:145861600-145869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:145861600-145870000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:145861800-145867600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:145861800-145870200	Weak transcription	Brain Substantia Nigra	brain
20	chr3:145861800-145870400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:145861800-145870800	Weak transcription	Pancreas	Pancrea
22	chr3:145861800-145872200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
25	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:145862000-145871600	Strong transcription	HSMM	muscle
28	chr3:145862000-145873800	Weak transcription	NHLF	lung
29	chr3:145862400-145874000	Weak transcription	Lung	lung
30	chr3:145862600-145870800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:145863600-145869000	Weak transcription	Fetal Stomach	stomach
32	chr3:145864400-145869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:145864400-145870800	Weak transcription	Esophagus	oesophagus
34	chr3:145864400-145870800	Weak transcription	Gastric	stomach
35	chr3:145864400-145872200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:145864400-145873000	Genic enhancers	Osteobl	bone
37	chr3:145864600-145870000	Weak transcription	Right Ventricle	heart
38	chr3:145864600-145870800	Weak transcription	Right Atrium	heart
39	chr3:145864800-145870400	Weak transcription	HMEC	breast
40	chr3:145865200-145869000	Enhancers	Rectal Smooth Muscle	rectum
41	chr3:145865600-145869000	Enhancers	Fetal Heart	heart
42	chr3:145865800-145869000	Weak transcription	Left Ventricle	heart
43	chr3:145865800-145870400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:145865800-145870800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:145866000-145867400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:145866200-145868200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr3:145866400-145867800	Enhancers	HUVEC	blood vessel
48	chr3:145866800-145867800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:145866800-145868400	Weak transcription	Ovary	ovary
50	chr3:145866800-145868600	Enhancers	Stomach Smooth Muscle	stomach

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