Variant report

Variant	rs1541629
Chromosome Location	chr12:106294365-106294366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106293395..106295805-chr12:106296043..106298389,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10507203	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861526	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861527	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861528	0.91[ASN][1000 genomes]
rs10861529	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861531	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11112776	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112791	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11615749	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12301955	0.91[EUR][1000 genomes]
rs12302909	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12307410	0.85[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12367295	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12368539	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12423582	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12426023	0.91[EUR][1000 genomes]
rs1345544	0.90[EUR][1000 genomes]
rs1345545	0.90[EUR][1000 genomes]
rs1421441	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421464	0.88[EUR][1000 genomes]
rs1421467	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17278606	0.90[EUR][1000 genomes]
rs1862027	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1862028	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895104	0.91[ASN][1000 genomes]
rs2374559	0.90[EUR][1000 genomes]
rs2374561	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28635481	0.87[EUR][1000 genomes]
rs4620812	0.87[EUR][1000 genomes]
rs7133626	0.90[EUR][1000 genomes]
rs7297930	0.90[EUR][1000 genomes]
rs7300496	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300906	0.90[EUR][1000 genomes]
rs7300926	0.90[EUR][1000 genomes]
rs7305359	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73387048	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7960296	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7960880	0.88[EUR][1000 genomes]
rs7964927	0.90[EUR][1000 genomes]
rs7968454	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968564	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980152	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1541629	GLT8D2	cis	cerebellum	SCAN
rs1541629	PAH	cis	parietal	SCAN
rs1541629	CHST11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106286400-106294400	Weak transcription	HSMMtube	muscle
2	chr12:106292400-106294400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:106292800-106305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:106293600-106294800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:106293600-106300000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links