Variant report

Variant	rs2864795
Chromosome Location	chr3:145873483-145873484
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53195198..53195701-chr3:145873151..145873651,2	Hela-S3	cervix:
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
ENSG00000163932	Chromatin interaction

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

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

rs_ID	r²[population]
rs11928424	0.87[ASN][1000 genomes]
rs17412259	0.85[EUR][1000 genomes]
rs34803917	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762690	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681295	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681296	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681298	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681300	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6780480	0.81[EUR][1000 genomes]
rs73148913	0.85[EUR][1000 genomes]
rs73148936	0.85[EUR][1000 genomes]
rs73148944	0.81[EUR][1000 genomes]
rs73148974	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148977	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148979	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148981	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148996	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148997	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148999	0.96[ASN][1000 genomes]
rs73149001	0.87[ASN][1000 genomes]
rs73150804	0.87[ASN][1000 genomes]
rs73150806	0.87[ASN][1000 genomes]
rs73150808	0.87[ASN][1000 genomes]
rs73150809	0.87[ASN][1000 genomes]
rs73150811	0.87[ASN][1000 genomes]
rs73150812	0.87[ASN][1000 genomes]
rs73150813	0.87[ASN][1000 genomes]
rs73150816	0.87[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
rs2864795	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:145871600-145873600	Weak transcription	Aorta	Aorta
38	chr3:145871600-145873600	Weak transcription	Right Atrium	heart
39	chr3:145871600-145873600	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:145871600-145873600	Weak transcription	HSMM	muscle
41	chr3:145871600-145873800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:145871600-145873800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:145871600-145873800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:145871600-145873800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:145871600-145873800	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:145871600-145873800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:145871600-145873800	Weak transcription	Fetal Kidney	kidney
48	chr3:145871600-145873800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:145871600-145873800	Enhancers	HepG2	liver
50	chr3:145871600-145874000	Weak transcription	Ovary	ovary

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