Variant report

Variant	rs4264700
Chromosome Location	chr3:134068462-134068463
allele	C/T
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	POLR2A	chr3:134068385-134068585	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134068339..134071562-chr3:134203031..134205941,6	MCF-7	breast:
2	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134066447..134072766-chr3:134202428..134206376,9	MCF-7	breast:
4	chr3:133967562..133971327-chr3:134067822..134072418,4	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10755085	0.89[CHB][hapmap]
rs1111516	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11708815	0.86[ASN][1000 genomes]
rs11719057	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs13075185	0.86[ASN][1000 genomes]
rs13322269	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1353778	0.89[CHB][hapmap]
rs1466827	1.00[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	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400279	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400280	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34341902	0.95[ASN][1000 genomes]
rs35951257	0.95[ASN][1000 genomes]
rs3732852	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773820	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821705	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4974485	0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974489	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974491	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974494	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974495	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974496	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4974497	0.95[ASN][1000 genomes]
rs4974498	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439477	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6439478	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6786148	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613066	0.86[ASN][1000 genomes]
rs9450	0.95[ASN][1000 genomes]
rs9817900	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[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

No data

Chromatin state (count:74 , 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	chr3:134061200-134069000	Weak transcription	Fetal Brain Female	brain
8	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
9	chr3:134065800-134069400	Weak transcription	Liver	Liver
10	chr3:134065800-134071400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:134065800-134071400	Enhancers	Fetal Intestine Large	intestine
12	chr3:134065800-134071600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:134065800-134072400	Weak transcription	Spleen	Spleen
14	chr3:134066000-134072800	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:134066200-134069400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:134066200-134069600	Weak transcription	A549	lung
17	chr3:134066200-134071000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:134066400-134071400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:134066400-134071600	Weak transcription	Fetal Lung	lung
20	chr3:134066400-134071600	Enhancers	Placenta	Placenta
21	chr3:134066400-134073000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:134066600-134069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:134066600-134071800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:134066800-134069600	Weak transcription	HepG2	liver
26	chr3:134066800-134073000	Weak transcription	Ovary	ovary
27	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
28	chr3:134067200-134068600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:134067200-134071600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:134067200-134071800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:134067200-134072000	Enhancers	HMEC	breast
32	chr3:134067200-134072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:134067200-134073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:134067400-134073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:134067400-134073200	Enhancers	Esophagus	oesophagus
36	chr3:134067600-134068600	Enhancers	Psoas Muscle	Psoas
37	chr3:134067600-134072800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:134067600-134073200	Weak transcription	Brain Angular Gyrus	brain
39	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
40	chr3:134067800-134069000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:134067800-134069800	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:134067800-134072400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:134067800-134073000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:134067800-134073200	Weak transcription	NH-A	brain
45	chr3:134068000-134069200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:134068000-134069200	Weak transcription	Stomach Mucosa	stomach
47	chr3:134068000-134069400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:134068000-134069400	Weak transcription	Right Atrium	heart
49	chr3:134068000-134069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:134068200-134069000	Weak transcription	Fetal Muscle Leg	muscle

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