Variant report

Variant	rs4974491
Chromosome Location	chr3:134055881-134055882
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	chr3:134034717..134037202-chr3:134054056..134056170,2	MCF-7	breast:
2	chr3:134052272..134054008-chr3:134054064..134057061,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1111516	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11708815	0.86[ASN][1000 genomes]
rs11719057	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs13075185	0.86[ASN][1000 genomes]
rs13322269	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1466827	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1498731	0.95[ASN][1000 genomes]
rs1603824	0.95[ASN][1000 genomes]
rs1863910	0.80[ASN][1000 genomes]
rs2133307	0.95[ASN][1000 genomes]
rs2400278	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400279	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400280	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34341902	0.95[ASN][1000 genomes]
rs35951257	0.95[ASN][1000 genomes]
rs3732852	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773820	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821705	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4264700	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974485	0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974489	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974494	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974495	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974496	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4974497	0.95[ASN][1000 genomes]
rs4974498	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439477	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6439478	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6786148	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613066	0.86[ASN][1000 genomes]
rs9450	0.95[ASN][1000 genomes]
rs9817900	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853621	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4974491	RP11-375I20.6	cis	Thyroid	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134035000-134058800	Weak transcription	Liver	Liver
2	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:134042000-134060800	Enhancers	Placenta	Placenta
4	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:134045000-134056400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:134049200-134060800	Enhancers	Fetal Intestine Large	intestine
7	chr3:134050600-134056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:134050600-134057000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:134050600-134060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:134050800-134061000	Weak transcription	Fetal Brain Female	brain
11	chr3:134051000-134056000	Enhancers	NHDF-Ad	bronchial
12	chr3:134051000-134056800	Enhancers	Osteobl	bone
13	chr3:134051200-134056600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:134051400-134056200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:134051400-134056200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:134051400-134058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:134051400-134058800	Weak transcription	Fetal Kidney	kidney
18	chr3:134052000-134056000	Enhancers	Fetal Intestine Small	intestine
19	chr3:134052200-134058600	Enhancers	Esophagus	oesophagus
20	chr3:134052400-134057400	Enhancers	Right Ventricle	heart
21	chr3:134052600-134057600	Enhancers	Pancreas	Pancrea
22	chr3:134052800-134058600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:134052800-134058800	Enhancers	HepG2	liver
24	chr3:134053000-134061200	Enhancers	Adipose Nuclei	Adipose
25	chr3:134053600-134057200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:134054000-134059600	Weak transcription	Colonic Mucosa	Colon
27	chr3:134054000-134064200	Weak transcription	Aorta	Aorta
28	chr3:134054200-134056000	Weak transcription	Spleen	Spleen
29	chr3:134054200-134057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:134054200-134058200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:134054200-134060200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:134054400-134057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:134054600-134061000	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:134055000-134056200	Enhancers	Stomach Mucosa	stomach
37	chr3:134055000-134056800	Enhancers	Left Ventricle	heart
38	chr3:134055000-134057000	Enhancers	A549	lung
39	chr3:134055000-134057200	Enhancers	Fetal Heart	heart
40	chr3:134055200-134056000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:134055200-134056000	Enhancers	Stomach Smooth Muscle	stomach
42	chr3:134055200-134056400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:134055200-134056400	Enhancers	HSMMtube	muscle
44	chr3:134055200-134056600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:134055200-134056600	Enhancers	HMEC	breast
46	chr3:134055200-134056600	Enhancers	NHEK	skin
47	chr3:134055200-134056800	Enhancers	Right Atrium	heart
48	chr3:134055200-134057000	Enhancers	Lung	lung
49	chr3:134055200-134057400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:134055200-134061400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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