Variant report

Variant	rs7305359
Chromosome Location	chr12:106306003-106306004
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	chr12:106305287..106307682-chr12:106312157..106314624,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10507203	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10861526	0.87[EUR][1000 genomes]
rs10861527	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10861529	0.81[EUR][1000 genomes]
rs10861530	0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10861531	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11112776	0.85[EUR][1000 genomes]
rs11112789	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112791	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615749	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12301955	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302909	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307410	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12367295	0.87[EUR][1000 genomes]
rs12368539	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12423582	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426023	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345544	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345545	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421441	0.92[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1421461	0.83[ASN][1000 genomes]
rs1421464	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421467	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541629	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17278606	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862027	0.87[EUR][1000 genomes]
rs1862028	0.87[EUR][1000 genomes]
rs2374559	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28635481	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4620812	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133626	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297930	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300496	0.86[EUR][1000 genomes]
rs7300906	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300926	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73387048	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960296	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7960880	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7964927	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968454	0.86[EUR][1000 genomes]
rs7968564	0.87[EUR][1000 genomes]
rs7980152	0.87[EUR][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
rs7305359	GLT8D2	cis	cerebellum	SCAN
rs7305359	PAH	cis	parietal	SCAN
rs7305359	CHST11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106302600-106307200	Weak transcription	Fetal Stomach	stomach
2	chr12:106304800-106306200	Enhancers	HMEC	breast
3	chr12:106305600-106306200	Enhancers	NHEK	skin
4	chr12:106305600-106306800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:106306000-106307600	Strong transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links