Variant report

Variant	rs3804659
Chromosome Location	chr3:145840968-145840969
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145832668..145836066-chr3:145839232..145841565,3	MCF-7	breast:
2	chr3:145839176..145842654-chr3:145877605..145880673,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12632001	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749282	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3792347	0.83[CHD][hapmap]
rs67406460	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6787634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73010484	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7642145	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9842865	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804659	PLOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
2	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
4	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:145814200-145841000	Weak transcription	Lung	lung
7	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
8	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
9	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
12	chr3:145827400-145842000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:145832600-145848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:145833600-145843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:145834200-145851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:145834400-145851400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:145834600-145841200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:145834600-145852800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:145835200-145851200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:145835200-145852200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:145835600-145843600	Weak transcription	NHEK	skin
24	chr3:145835600-145851200	Weak transcription	Fetal Kidney	kidney
25	chr3:145835800-145843200	Weak transcription	Small Intestine	intestine
26	chr3:145835800-145846000	Weak transcription	Fetal Intestine Small	intestine
27	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
28	chr3:145836000-145852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:145836200-145844200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:145836800-145844000	Weak transcription	NHLF	lung
31	chr3:145837000-145841800	Weak transcription	Placenta	Placenta
32	chr3:145837000-145843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:145837000-145843200	Weak transcription	Esophagus	oesophagus
34	chr3:145837000-145844200	Weak transcription	NHDF-Ad	bronchial
35	chr3:145837000-145848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:145837000-145852400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:145837200-145842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:145837200-145845800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:145837200-145846000	Weak transcription	Adipose Nuclei	Adipose
40	chr3:145837200-145846000	Weak transcription	Fetal Lung	lung
41	chr3:145837200-145851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:145838200-145842200	Strong transcription	HUVEC	blood vessel
43	chr3:145838400-145841800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr3:145838400-145842000	Strong transcription	Osteobl	bone
45	chr3:145838600-145841000	Strong transcription	HepG2	liver
46	chr3:145838800-145842000	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr3:145838800-145843200	Strong transcription	HSMM	muscle
48	chr3:145839200-145845200	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:145839400-145841400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:145839400-145847600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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