Variant report

Variant	rs62336792
Chromosome Location	chr4:53729429-53729430
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	TAF7	chr4:53728148-53729570	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr4:53729310-53731670	SK-N-SH	brain:	n/a	chr4:53730198-53730206
3	SIN3A	chr4:53726721-53729851	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr4:53726951-53732052	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr4:53727789-53729591	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr4:53727338-53729596	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:53729423-53729542	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:
2	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000264585	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000248375	Chromatin interaction
ENSG00000226950	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10001855	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008073	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10014464	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043975	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11930907	0.87[ASN][1000 genomes]
rs11934293	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11941562	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483685	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483686	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1483687	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17082081	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17082143	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082147	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963003	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003198	0.87[ASN][1000 genomes]
rs2017237	0.88[ASN][1000 genomes]
rs2046364	0.88[ASN][1000 genomes]
rs2062253	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2200226	0.90[ASN][1000 genomes]
rs2279334	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306601	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2411259	0.81[EUR][1000 genomes]
rs2411281	0.86[ASN][1000 genomes]
rs28419463	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28454903	0.81[EUR][1000 genomes]
rs28489424	0.81[EUR][1000 genomes]
rs28526700	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28704139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733375	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28735908	0.81[EUR][1000 genomes]
rs28811693	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2898681	0.86[ASN][1000 genomes]
rs301135	0.83[AMR][1000 genomes]
rs301136	0.83[AMR][1000 genomes]
rs4242020	0.81[EUR][1000 genomes]
rs4309903	0.81[EUR][1000 genomes]
rs4864673	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4864679	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864681	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864682	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864688	0.88[ASN][1000 genomes]
rs4864690	0.87[ASN][1000 genomes]
rs4864691	0.87[ASN][1000 genomes]
rs4865422	0.81[EUR][1000 genomes]
rs4990628	0.81[EUR][1000 genomes]
rs5012592	0.81[EUR][1000 genomes]
rs59649036	0.88[ASN][1000 genomes]
rs61268502	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62336785	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336788	0.97[EUR][1000 genomes]
rs62336791	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62336794	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62336795	0.88[ASN][1000 genomes]
rs62336823	0.84[ASN][1000 genomes]
rs62338801	0.81[EUR][1000 genomes]
rs62338805	0.81[EUR][1000 genomes]
rs6833096	0.87[ASN][1000 genomes]
rs6839084	0.86[ASN][1000 genomes]
rs6852148	0.88[ASN][1000 genomes]
rs73143042	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900607	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs922932	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9993034	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53727400-53729600	Active TSS	Brain Angular Gyrus	brain
2	chr4:53727400-53729600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:53727600-53729600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:53727600-53729600	Active TSS	NHDF-Ad	bronchial
5	chr4:53727800-53730800	Active TSS	Aorta	Aorta
6	chr4:53727800-53731800	Active TSS	Fetal Kidney	kidney
7	chr4:53728000-53729600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:53728000-53729600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:53728000-53729800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:53728000-53730000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr4:53728000-53730000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:53728000-53730200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:53728000-53730400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:53728200-53729600	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr4:53728200-53729600	Active TSS	Fetal Brain Female	brain
16	chr4:53728200-53729800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:53728200-53729800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:53728200-53729800	Active TSS	Fetal Heart	heart
19	chr4:53728600-53730200	Active TSS	Right Atrium	heart
20	chr4:53728800-53729600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:53728800-53729600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:53728800-53729600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
23	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
25	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr4:53728800-53729800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
27	chr4:53728800-53730000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
28	chr4:53728800-53730000	Flanking Active TSS	Fetal Brain Male	brain
29	chr4:53728800-53730000	Flanking Active TSS	Placenta	Placenta
30	chr4:53728800-53731000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
31	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
32	chr4:53729200-53729600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr4:53729200-53729600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:53729200-53729600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:53729200-53729600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr4:53729200-53729600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:53729200-53729600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr4:53729200-53729600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
39	chr4:53729200-53729600	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr4:53729200-53729600	Enhancers	K562	blood
41	chr4:53729200-53730200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
42	chr4:53729200-53731800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr4:53729200-53732000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
44	chr4:53729200-53734200	Weak transcription	Psoas Muscle	Psoas
45	chr4:53729200-53734400	Weak transcription	HSMMtube	muscle
46	chr4:53729200-53735200	Weak transcription	Colonic Mucosa	Colon
47	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
48	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
49	chr4:53729400-53729600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:53729400-53729600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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