Variant report

Variant	rs4924354
Chromosome Location	chr15:39736624-39736625
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39731790..39738265-chr15:39871818..39875275,7	MCF-7	breast:
2	chr15:39735362..39737088-chr15:39871158..39872700,2	MCF-7	breast:
3	chr15:39721562..39724453-chr15:39734811..39737253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11070202	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906753	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907239	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16969088	0.87[EUR][1000 genomes]
rs4244569	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4306475	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4344715	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4405525	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4417529	0.80[ASN][1000 genomes]
rs4522393	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4923826	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55638424	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57817952	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58084121	0.82[EUR][1000 genomes]
rs59238363	0.84[EUR][1000 genomes]
rs6492889	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724098	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8026812	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029673	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032895	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924354	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39727200-39746800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:39727800-39740200	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:39728400-39739400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:39731000-39736800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:39731400-39736800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:39731600-39737400	Weak transcription	Fetal Thymus	thymus
7	chr15:39731600-39739400	Weak transcription	HepG2	liver
8	chr15:39734600-39737400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:39734800-39739400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:39736600-39737200	Enhancers	Fetal Muscle Trunk	muscle
11	chr15:39736600-39737800	Enhancers	Colon Smooth Muscle	Colon

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