Variant report

Variant	rs7249532
Chromosome Location	chr19:38753385-38753386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr19:38753372-38754066	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr19:38753342-38753895	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr19:38753294-38754054	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38753173..38754676-chr19:38892470..38894801,2	MCF-7	breast:
3	chr19:38752235..38756779-chr19:38783718..38786830,7	MCF-7	breast:
4	chr19:38751509..38754892-chr19:38775183..38778816,3	K562	blood:
5	chr19:38753341..38760825-chr19:38779856..38783291,10	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
SPINT2	TF binding region
ENSG00000200209	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10993	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880301	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880326	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880459	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745948	0.88[ASN][1000 genomes]
rs59648079	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60163114	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508780	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253827	0.84[EUR][1000 genomes]
rs7260295	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030303	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030307	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030308	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030309	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030311	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8101482	0.91[ASN][1000 genomes]
rs8111378	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112201	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38747600-38753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38747600-38754200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:38748000-38753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr19:38748000-38753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:38748000-38753400	Weak transcription	K562	blood
6	chr19:38748000-38753600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:38748000-38754400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:38749000-38754400	Weak transcription	Fetal Brain Female	brain
9	chr19:38749200-38754400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:38751600-38754400	Weak transcription	NHLF	lung
11	chr19:38752200-38754600	Enhancers	Placenta	Placenta
12	chr19:38752800-38754200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:38753000-38753800	Enhancers	A549	lung
14	chr19:38753200-38754600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:38753200-38754600	Enhancers	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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