Variant report

Variant	rs7960213
Chromosome Location	chr12:60270532-60270533
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	chr12:60264304..60266697-chr12:60268943..60270988,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10082980	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10083053	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747857	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784011	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784012	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877358	0.89[ASN][1000 genomes]
rs10877366	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11173232	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11173234	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12231000	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426916	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12578830	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4132660	0.87[EUR][1000 genomes]
rs4326838	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4415809	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4469929	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4474476	0.92[EUR][1000 genomes]
rs4603345	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4630332	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4635120	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758751	0.89[ASN][1000 genomes]
rs7301335	0.86[EUR][1000 genomes]
rs7302440	0.81[EUR][1000 genomes]
rs73119606	0.95[EUR][1000 genomes]
rs7315756	0.89[ASN][1000 genomes]
rs7957469	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961087	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7971243	0.88[EUR][1000 genomes];0.82[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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751107	chr12:60252000-60353533	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1050201	chr12:60269149-60297702	Weak transcription Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1055021	chr12:60269149-60302823	Enhancers Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7960213	R3HDM2	cis	cerebellum	SCAN
rs7960213	BLOC1S1	cis	cerebellum	SCAN
rs7960213	DNAJC14	cis	cerebellum	SCAN
rs7960213	OR6C75	cis	parietal	SCAN
rs7960213	STAT2	cis	cerebellum	SCAN
rs7960213	MMP19	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60242200-60295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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