Variant report

Variant	rs1498731
Chromosome Location	chr3:134068179-134068180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134067230-134068922	IMR90	lung:	n/a	n/a
2	TEAD4	chr3:134067319-134068189	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:134067277-134068309	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134066447..134072766-chr3:134202428..134206376,9	MCF-7	breast:
3	chr3:133967562..133971327-chr3:134067822..134072418,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260633	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000163785	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1111516	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.90[ASN][1000 genomes]
rs11719057	0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs1353776	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466827	0.86[ASN][1000 genomes]
rs1603824	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400278	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	0.90[ASN][1000 genomes]
rs3821705	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.95[ASN][1000 genomes]
rs4974485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[ASN][1000 genomes]
rs4974494	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974495	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.90[ASN][1000 genomes]
rs9450	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1498731	RP11-375I20.6	cis	lung	GTEx
rs1498731	RP11-375I20.6	cis	Thyroid	GTEx
rs1498731	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs1498731	RP11-375I20.6	cis	Artery Aorta	GTEx
rs1498731	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs1498731	RP11-375I20.6	cis	Artery Tibial	GTEx
rs1498731	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs1498731	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs1498731	RP11-375I20.6	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:134058600-134069200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:134060600-134070000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:134060800-134072200	Weak transcription	Fetal Kidney	kidney
7	chr3:134061200-134068400	Weak transcription	Fetal Stomach	stomach
8	chr3:134061200-134069000	Weak transcription	Fetal Brain Female	brain
9	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
10	chr3:134065800-134069400	Weak transcription	Liver	Liver
11	chr3:134065800-134071400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:134065800-134071400	Enhancers	Fetal Intestine Large	intestine
13	chr3:134065800-134071600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:134065800-134072400	Weak transcription	Spleen	Spleen
15	chr3:134066000-134068400	Enhancers	Fetal Intestine Small	intestine
16	chr3:134066000-134072800	Enhancers	Duodenum Mucosa	Duodenum
17	chr3:134066200-134068400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:134066200-134069400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:134066200-134069600	Weak transcription	A549	lung
20	chr3:134066200-134071000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:134066400-134068200	Enhancers	Gastric	stomach
22	chr3:134066400-134071400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:134066400-134071600	Weak transcription	Fetal Lung	lung
24	chr3:134066400-134071600	Enhancers	Placenta	Placenta
25	chr3:134066400-134073000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:134066600-134068200	Enhancers	Aorta	Aorta
27	chr3:134066600-134068200	Enhancers	Fetal Muscle Leg	muscle
28	chr3:134066600-134068200	Enhancers	HSMMtube	muscle
29	chr3:134066600-134069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:134066600-134071800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:134066800-134069600	Weak transcription	HepG2	liver
33	chr3:134066800-134073000	Weak transcription	Ovary	ovary
34	chr3:134067000-134068200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:134067000-134068200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:134067000-134068200	Enhancers	Left Ventricle	heart
37	chr3:134067000-134068200	Enhancers	HSMM	muscle
38	chr3:134067000-134068200	Enhancers	Osteobl	bone
39	chr3:134067000-134068400	Enhancers	NHDF-Ad	bronchial
40	chr3:134067000-134068400	Enhancers	NHEK	skin
41	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
42	chr3:134067200-134068200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:134067200-134068200	Enhancers	Right Ventricle	heart
44	chr3:134067200-134068400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:134067200-134068600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:134067200-134071600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:134067200-134071800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:134067200-134072000	Enhancers	HMEC	breast
49	chr3:134067200-134072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:134067200-134073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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