Variant report

Variant	rs1544454
Chromosome Location	chr7:26635812-26635813
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26625340..26627704-chr7:26633825..26636063,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10247053	0.88[ASN][1000 genomes]
rs10254403	0.88[ASN][1000 genomes]
rs10258273	0.95[ASN][1000 genomes]
rs12536073	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12538653	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12538703	0.94[ASN][1000 genomes]
rs12538778	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17286978	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17287580	0.95[ASN][1000 genomes]
rs17359666	0.95[ASN][1000 genomes]
rs2214810	0.95[ASN][1000 genomes]
rs4722621	0.95[ASN][1000 genomes]
rs4722622	0.95[ASN][1000 genomes]
rs58869468	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61267197	0.95[ASN][1000 genomes]
rs6944839	0.95[ASN][1000 genomes]
rs6945115	0.95[ASN][1000 genomes]
rs6964688	0.95[ASN][1000 genomes]
rs73071985	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7777206	0.91[EUR][1000 genomes]
rs7782566	0.95[ASN][1000 genomes]
rs7797096	0.81[EUR][1000 genomes];0.90[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	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv830929	chr7:26587888-26749735	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1544454	SKAP2	cis	lymphoblastoid	seeQTL
rs1544454	HOXA9	cis	parietal	SCAN
rs1544454	NPVF	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26633600-26636200	Enhancers	Fetal Stomach	stomach
2	chr7:26634400-26639400	Weak transcription	Fetal Kidney	kidney
3	chr7:26634400-26656600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:26635400-26636000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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