Variant report

Variant	rs4681301
Chromosome Location	chr3:145876406-145876407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:56286022..56288671-chr3:145875051..145877020,2	MCF-7	breast:
2	chr3:145787365..145792721-chr3:145875341..145880381,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124225	Chromatin interaction
ENSG00000152952	Chromatin interaction

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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935608	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1170389	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1170390	0.83[JPT][hapmap]
rs1170391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1170392	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1170393	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11718741	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]
rs11927021	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498084	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13087364	0.84[JPT][hapmap]
rs13088646	0.89[JPT][hapmap]
rs1375588	0.84[EUR][1000 genomes]
rs1375591	0.83[JPT][hapmap]
rs1707468	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1707469	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17413767	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17414130	0.80[JPT][hapmap]
rs1868541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1913186	0.94[JPT][hapmap]
rs1982382	0.82[JPT][hapmap]
rs2137485	0.83[ASN][1000 genomes]
rs34800183	0.81[ASN][1000 genomes]
rs4681297	0.83[JPT][hapmap]
rs56842856	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57327675	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57945878	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60267871	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60811409	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61050446	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61154334	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73148985	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73148986	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73148991	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613150	0.83[JPT][hapmap]
rs7623263	0.89[JPT][hapmap]
rs7642940	0.84[JPT][hapmap]
rs965032	0.96[EUR][1000 genomes];0.88[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
rs4681301	PLOD2	cis	Muscle Skeletal	GTEx
rs4681301	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145870600-145876800	Weak transcription	Hela-S3	cervix
2	chr3:145870800-145876800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:145871400-145877800	Weak transcription	Gastric	stomach
4	chr3:145871600-145876800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:145871600-145877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:145871600-145877600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:145871800-145876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:145873000-145877600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:145873600-145876600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:145873600-145879800	Active TSS	Stomach Smooth Muscle	stomach
11	chr3:145873800-145876800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:145873800-145876800	Enhancers	Fetal Lung	lung
13	chr3:145873800-145877000	Flanking Active TSS	HUVEC	blood vessel
14	chr3:145874000-145876800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:145874000-145876800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:145874000-145876800	Enhancers	Brain Angular Gyrus	brain
17	chr3:145874000-145877000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:145874000-145877800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:145874200-145878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:145874200-145880000	Active TSS	Right Ventricle	heart
21	chr3:145874400-145877000	Transcr. at gene 5' and 3'	Osteobl	bone
22	chr3:145874600-145876800	Transcr. at gene 5' and 3'	HSMM	muscle
23	chr3:145874600-145877800	Weak transcription	Pancreas	Pancrea
24	chr3:145874600-145878000	Weak transcription	Lung	lung
25	chr3:145874600-145878000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:145874800-145876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:145874800-145877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:145874800-145877800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:145874800-145878000	Weak transcription	Stomach Mucosa	stomach
30	chr3:145874800-145880000	Active TSS	Ovary	ovary
31	chr3:145874800-145880000	Active TSS	Right Atrium	heart
32	chr3:145874800-145880600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:145875000-145876600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:145875000-145876800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:145875000-145876800	Weak transcription	Colonic Mucosa	Colon
36	chr3:145875000-145877400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:145875000-145877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:145875000-145877600	Weak transcription	Psoas Muscle	Psoas
39	chr3:145875000-145878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:145875000-145880400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:145875200-145877000	Flanking Active TSS	Fetal Heart	heart
42	chr3:145875400-145876600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:145875400-145876800	Enhancers	Brain Substantia Nigra	brain
44	chr3:145875600-145876800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
45	chr3:145875600-145876800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:145875600-145876800	Enhancers	Left Ventricle	heart
47	chr3:145875600-145877000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:145875600-145880000	Active TSS	A549	lung
49	chr3:145875800-145876600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:145875800-145876600	Enhancers	Small Intestine	intestine

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