Variant report

Variant	rs12138486
Chromosome Location	chr1:93865391-93865392
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	chr1:93809889..93812256-chr1:93863912..93865859,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10443193	0.84[EUR][1000 genomes]
rs10874777	0.87[ASN][1000 genomes]
rs10874778	1.00[ASN][1000 genomes]
rs10874783	0.83[EUR][1000 genomes]
rs10874784	0.83[EUR][1000 genomes]
rs11164908	0.81[CEU][hapmap]
rs11164916	0.87[ASN][1000 genomes]
rs11164921	0.84[EUR][1000 genomes]
rs11164924	0.81[ASN][1000 genomes]
rs11164938	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11576494	0.82[ASN][1000 genomes]
rs12030549	0.84[JPT][hapmap]
rs12030843	0.81[CEU][hapmap]
rs12044557	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs12044883	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12133576	0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12133907	0.86[ASN][1000 genomes]
rs12135266	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs12406245	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12563120	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs12742850	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12752223	0.83[ASN][1000 genomes]
rs1426318	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1559828	0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1593512	0.87[ASN][1000 genomes]
rs1812668	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2031225	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs2031226	0.83[JPT][hapmap]
rs2114271	0.84[EUR][1000 genomes]
rs2114272	0.83[EUR][1000 genomes]
rs2114273	0.84[ASN][1000 genomes]
rs2162276	0.83[EUR][1000 genomes]
rs2296558	0.84[JPT][hapmap]
rs2391256	1.00[ASN][1000 genomes]
rs2391271	0.89[JPT][hapmap]
rs2765545	0.86[CHD][hapmap]
rs2783499	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs2783500	0.81[CEU][hapmap]
rs2783501	0.81[CEU][hapmap]
rs35102250	0.80[ASN][1000 genomes]
rs3754186	0.84[JPT][hapmap]
rs3767962	0.82[ASN][1000 genomes]
rs3767964	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3767967	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4000699	0.84[JPT][hapmap]
rs4240966	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs4484937	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs4847240	0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4847241	0.84[EUR][1000 genomes]
rs4847242	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs4847245	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4847408	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs4847412	0.82[ASN][1000 genomes]
rs4847419	0.86[ASN][1000 genomes]
rs4847420	0.86[ASN][1000 genomes]
rs4847426	0.84[EUR][1000 genomes]
rs4847428	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs531358	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs59417472	0.86[ASN][1000 genomes]
rs612037	0.84[JPT][hapmap]
rs622608	0.94[JPT][hapmap]
rs637646	0.94[JPT][hapmap]
rs6541349	0.81[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs6541401	0.84[JPT][hapmap]
rs6541404	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs6658257	0.82[ASN][1000 genomes]
rs6680022	0.83[ASN][1000 genomes]
rs6691545	0.84[EUR][1000 genomes]
rs6694508	0.83[ASN][1000 genomes]
rs6703310	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs687394	0.81[JPT][hapmap]
rs693737	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs7417952	0.87[ASN][1000 genomes]
rs7525248	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs771481	0.93[CEU][hapmap]
rs797668	0.84[JPT][hapmap]
rs942196	0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12138486	GBP5	cis	parietal	SCAN
rs12138486	GLMN	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93853200-93866000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93861000-93865400	Weak transcription	HMEC	breast
3	chr1:93862000-93865400	Weak transcription	HepG2	liver
4	chr1:93865200-93865600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:93865200-93865600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:93865200-93865600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:93865200-93865800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:93865200-93865800	Enhancers	NHEK	skin

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