Variant report

Variant	rs12541299
Chromosome Location	chr8:86211927-86211928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:86211093..86212034-chr8:86283049..86283804,4	MCF-7	breast:
2	chr8:86211080..86212132-chr8:86363695..86364436,5	MCF-7	breast:
3	chr8:86211068..86212027-chr8:87100896..87101631,2	K562	blood:
4	chr8:86211585..86214496-chr8:87045992..87048546,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10090196	0.82[EUR][1000 genomes]
rs10091582	0.99[ASN][1000 genomes]
rs10097917	0.83[ASN][1000 genomes]
rs10099251	0.99[ASN][1000 genomes]
rs10106970	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10107686	0.93[ASN][1000 genomes]
rs10110461	0.98[ASN][1000 genomes]
rs10111971	0.99[ASN][1000 genomes]
rs1014303	0.82[ASN][1000 genomes]
rs1021583	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11261469	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11261471	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11261472	0.82[ASN][1000 genomes]
rs11989660	0.82[ASN][1000 genomes]
rs12114575	0.81[ASN][1000 genomes]
rs12541445	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543256	0.90[ASN][1000 genomes]
rs12544332	0.88[ASN][1000 genomes]
rs12546106	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12550160	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12679400	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13259464	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1496531	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1496532	0.88[ASN][1000 genomes]
rs1496533	0.94[ASN][1000 genomes]
rs1553015	0.82[ASN][1000 genomes]
rs1553016	0.99[ASN][1000 genomes]
rs1553017	0.98[ASN][1000 genomes]
rs16913681	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16913721	0.93[EUR][1000 genomes]
rs17740658	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1809819	0.94[ASN][1000 genomes]
rs1845891	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1845892	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1908762	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1995057	0.88[ASN][1000 genomes]
rs2006767	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132589	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132590	0.92[ASN][1000 genomes]
rs2220972	0.87[ASN][1000 genomes]
rs2279700	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279701	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291786	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291787	0.93[ASN][1000 genomes]
rs28374336	0.99[ASN][1000 genomes]
rs28377260	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28439950	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28564613	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28677919	0.83[EUR][1000 genomes]
rs35285802	0.83[EUR][1000 genomes]
rs35558766	0.98[ASN][1000 genomes]
rs3779901	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150962	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150964	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4150974	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150977	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4609189	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4617148	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4739698	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4739702	0.82[ASN][1000 genomes]
rs4740045	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4740047	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4740048	0.84[ASN][1000 genomes]
rs6605610	0.84[ASN][1000 genomes]
rs6605611	0.84[ASN][1000 genomes]
rs6605613	0.98[ASN][1000 genomes]
rs6993316	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6994113	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7001359	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7004871	0.93[EUR][1000 genomes]
rs7011001	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7821629	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7826511	0.91[ASN][1000 genomes]
rs7827175	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7829240	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7835303	0.81[ASN][1000 genomes]
rs7839129	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903896	0.82[ASN][1000 genomes]
rs903897	0.81[ASN][1000 genomes]
rs9329908	0.96[EUR][1000 genomes];0.93[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	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2761442	chr8:86201657-86230641	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12541299	LRRCC1	cis	Artery Tibial	GTEx
rs12541299	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs12541299	LRRCC1	cis	Esophagus Mucosa	GTEx
rs12541299	C8orf59	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86197400-86225800	Weak transcription	Fetal Intestine Small	intestine
2	chr8:86208800-86217200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:86210400-86216000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr8:86211400-86216600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr8:86211600-86222000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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