Variant report

Variant	rs35951257
Chromosome Location	chr3:134063479-134063480
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	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466827	0.86[ASN][1000 genomes]
rs1498731	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400278	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	0.90[ASN][1000 genomes]
rs3821705	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.95[ASN][1000 genomes]
rs4974485	0.98[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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974495	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.90[ASN][1000 genomes]
rs9450	0.86[AMR][1000 genomes];0.93[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
rs35951257	RP11-375I20.6	cis	lung	GTEx
rs35951257	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs35951257	RP11-375I20.6	cis	Artery Tibial	GTEx
rs35951257	RP11-375I20.6	cis	Thyroid	GTEx
rs35951257	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs35951257	RP11-375I20.6	cis	Artery Aorta	GTEx
rs35951257	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs35951257	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs35951257	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134054000-134064200	Weak transcription	Aorta	Aorta
2	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:134056200-134066600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:134056400-134064800	Weak transcription	Ovary	ovary
7	chr3:134057200-134067400	Weak transcription	Fetal Heart	heart
8	chr3:134058400-134065000	Weak transcription	Gastric	stomach
9	chr3:134058400-134065200	Weak transcription	Right Ventricle	heart
10	chr3:134058600-134069200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:134059200-134064200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:134059200-134065200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:134059800-134065200	Weak transcription	A549	lung
14	chr3:134060600-134065000	Weak transcription	HSMM	muscle
15	chr3:134060600-134065200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:134060600-134065200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:134060600-134065200	Weak transcription	Osteobl	bone
18	chr3:134060600-134067200	Weak transcription	Lung	lung
19	chr3:134060600-134067800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:134060600-134070000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:134060800-134065000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:134060800-134067200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:134060800-134072200	Weak transcription	Fetal Kidney	kidney
24	chr3:134061200-134064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:134061200-134068400	Weak transcription	Fetal Stomach	stomach
26	chr3:134061200-134069000	Weak transcription	Fetal Brain Female	brain
27	chr3:134061400-134064000	Weak transcription	Placenta	Placenta
28	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
29	chr3:134062600-134065400	Weak transcription	Liver	Liver
30	chr3:134063000-134065000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:134063200-134064600	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:134063200-134064600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:134063400-134063600	Enhancers	Pancreas	Pancrea
34	chr3:134063400-134063600	Enhancers	Psoas Muscle	Psoas
35	chr3:134063400-134064000	Enhancers	GM12878-XiMat	blood
36	chr3:134063400-134064600	Enhancers	Spleen	Spleen
37	chr3:134063400-134065000	Weak transcription	Adipose Nuclei	Adipose

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