Variant report

Variant	rs12056107
Chromosome Location	chr7:137892248-137892249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:137891304..137893793-chr7:138144559..138146749,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122779	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1074097	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11761097	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771299	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13221593	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13223602	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13232998	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13235037	0.81[GIH][hapmap]
rs1387582	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1602105	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28773312	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35133614	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3950563	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4031450	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4031455	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4634568	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56302303	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6467743	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6467744	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6467745	0.92[ASN][1000 genomes]
rs6467746	0.92[ASN][1000 genomes]
rs6943019	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958867	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965586	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7778052	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7787722	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7793307	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831152	chr7:137884311-138033117	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12056107	BPGM	cis	cerebellum	SCAN
rs12056107	STRA8	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137873600-137893800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:137880400-137893800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:137888600-137892600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:137888600-137893200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:137890200-137893200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:137890600-137892600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:137891000-137892400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:137891000-137893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:137891000-137893600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr7:137891000-137894200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:137891600-137894000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr7:137892000-137892400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr7:137892000-137892600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:137892000-137893400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:137892000-137893800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:137892000-137894400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr7:137892000-137894400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr7:137892000-137895400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:137892200-137892400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:137892200-137892600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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