Variant report

Variant	rs4681295
Chromosome Location	chr3:145832664-145832665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145831639..145836013-chr3:145876068..145880595,7	MCF-7	breast:
2	chr3:145832521..145835172-chr3:145842139..145845404,4	MCF-7	breast:
3	chr3:145786878..145789402-chr3:145831602..145833986,2	MCF-7	breast:
4	chr3:145829569..145840903-chr3:145873254..145880972,31	MCF-7	breast:
5	chr3:145832179..145836696-chr3:145881447..145885871,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction
ENSG00000240032	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11928424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17412259	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2864795	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34803917	0.94[EUR][1000 genomes]
rs3762690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780480	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73148913	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73148936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148944	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73148974	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148977	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148979	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148981	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148992	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148994	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148996	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73148997	0.97[EUR][1000 genomes];0.83[ASN][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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4681295	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 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	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
5	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
7	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:145814200-145841000	Weak transcription	Lung	lung
11	chr3:145816000-145836800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon
13	chr3:145819800-145841800	Weak transcription	Fetal Heart	heart
14	chr3:145819800-145849200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:145820000-145834000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:145821000-145849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:145821200-145835200	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:145821200-145835400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:145822200-145833800	Weak transcription	Fetal Kidney	kidney
20	chr3:145822800-145836800	Weak transcription	Ovary	ovary
21	chr3:145824600-145835000	Weak transcription	HMEC	breast
22	chr3:145824600-145839600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:145825000-145835400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:145826800-145833200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:145827000-145855200	Weak transcription	Aorta	Aorta
26	chr3:145827400-145833600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:145827400-145836600	Weak transcription	Adipose Nuclei	Adipose
28	chr3:145827400-145836600	Weak transcription	HSMMtube	muscle
29	chr3:145827400-145840200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:145827400-145842000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:145828000-145833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:145828400-145833000	Weak transcription	HUVEC	blood vessel
33	chr3:145828400-145833400	Weak transcription	NH-A	brain
34	chr3:145828600-145837200	Strong transcription	HSMM	muscle
35	chr3:145830200-145832800	Weak transcription	Liver	Liver
36	chr3:145830200-145833000	Weak transcription	A549	lung
37	chr3:145831400-145848400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:145831600-145834600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
39	chr3:145831800-145834600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:145832000-145835000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr3:145832000-145836800	Weak transcription	Placenta	Placenta
42	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:145832200-145835600	Weak transcription	Psoas Muscle	Psoas
44	chr3:145832200-145836800	Weak transcription	Left Ventricle	heart
45	chr3:145832200-145838400	Weak transcription	Fetal Stomach	stomach
46	chr3:145832400-145834200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:145832400-145834600	Enhancers	HepG2	liver
48	chr3:145832400-145835000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:145832400-145835400	Strong transcription	Osteobl	bone
50	chr3:145832600-145833000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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