Variant report

Variant	rs236330
Chromosome Location	chr1:94059554-94059555
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	FOXA1	chr1:94059364-94059734	T-47D	breast:	n/a	chr1:94059431-94059443
2	MXI1	chr1:94058292-94059611	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:94059425-94059629	HepG2	liver:	n/a	n/a
4	EP300	chr1:94059388-94059949	T-47D	breast:	n/a	n/a
5	HEY1	chr1:94059174-94059709	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:94059513-94060378	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:94059421-94059735	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:94059208-94059901	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:94059333-94060038	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:94059467-94060440	HepG2	liver:	n/a	n/a
11	TCF7L2	chr1:94059395-94059767	MCF-7	breast:	n/a	chr1:94059500-94059516 chr1:94059500-94059516

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000224093	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17110124	0.94[ASN][1000 genomes]
rs2281474	0.92[ASN][1000 genomes]
rs2295330	0.90[CHB][hapmap]
rs236321	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs236322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236323	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236326	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236329	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236331	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs236332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236333	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236335	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767973	0.91[ASN][1000 genomes]
rs3767975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3767976	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3767977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57012808	0.92[ASN][1000 genomes]
rs57466479	0.91[ASN][1000 genomes]
rs57914444	0.91[ASN][1000 genomes]
rs59777284	0.91[ASN][1000 genomes]
rs6661488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671749	0.97[ASN][1000 genomes]
rs6674143	0.90[CHB][hapmap]
rs6692801	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516400	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518795	0.95[ASN][1000 genomes]
rs7519939	0.97[ASN][1000 genomes]
rs7524368	0.91[ASN][1000 genomes]
rs7551964	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236330	BCAR3	cis	parietal	SCAN
rs236330	EPHX4	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
6	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:94055800-94061000	Weak transcription	Aorta	Aorta
9	chr1:94056000-94066000	Weak transcription	Ovary	ovary
10	chr1:94056800-94060200	Enhancers	Pancreas	Pancrea
11	chr1:94057000-94060200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:94057000-94060200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:94057000-94060200	Genic enhancers	HMEC	breast
14	chr1:94057200-94060000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr1:94057200-94060200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:94057200-94060400	Enhancers	Left Ventricle	heart
17	chr1:94057200-94060400	Enhancers	Psoas Muscle	Psoas
18	chr1:94057400-94068000	Genic enhancers	HSMM	muscle
19	chr1:94057400-94069200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:94057400-94071000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:94057600-94061000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:94057800-94059600	Weak transcription	Osteobl	bone
24	chr1:94057800-94059800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:94057800-94060200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:94057800-94060200	Enhancers	Esophagus	oesophagus
27	chr1:94057800-94061800	Enhancers	Placenta	Placenta
28	chr1:94058000-94059600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:94058000-94059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:94058000-94059800	Weak transcription	Fetal Thymus	thymus
31	chr1:94058000-94060000	Bivalent Enhancer	Fetal Heart	heart
32	chr1:94058000-94060000	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:94058000-94060200	Enhancers	Right Atrium	heart
34	chr1:94058000-94062000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:94058000-94062800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:94058000-94062800	Genic enhancers	NHEK	skin
37	chr1:94058000-94066600	Enhancers	Adipose Nuclei	Adipose
38	chr1:94058000-94066600	Enhancers	Fetal Muscle Leg	muscle
39	chr1:94058200-94059800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:94058200-94060800	Weak transcription	NH-A	brain
41	chr1:94058200-94061400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:94058200-94064600	Weak transcription	HUVEC	blood vessel
43	chr1:94058200-94065000	Enhancers	Colon Smooth Muscle	Colon
44	chr1:94058400-94059600	Weak transcription	Fetal Lung	lung
45	chr1:94058400-94059800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:94058400-94059800	Weak transcription	HSMMtube	muscle
47	chr1:94058400-94060000	Enhancers	Fetal Stomach	stomach
48	chr1:94058400-94060200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:94058400-94060200	Enhancers	Gastric	stomach
50	chr1:94058400-94060400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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