Variant report

Variant	rs12662500
Chromosome Location	chr6:54595728-54595729
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:54594502..54597427-chr6:54632424..54633945,2	MCF-7	breast:
2	chr6:54591002..54596706-chr6:54709941..54714732,14	MCF-7	breast:
3	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
4	chr6:54588605..54590894-chr6:54594243..54596836,3	MCF-7	breast:
5	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
6	chr6:54589684..54593022-chr6:54593846..54596999,3	MCF-7	breast:
7	chr6:54594451..54596147-chr6:54739921..54742591,2	MCF-7	breast:
8	chr6:54594616..54597518-chr6:54631395..54633965,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10085187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1018140	0.91[ASN][1000 genomes]
rs1039694	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1039695	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10738112	0.84[ASN][1000 genomes]
rs10738113	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10807478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948832	0.91[ASN][1000 genomes]
rs12210278	0.91[ASN][1000 genomes]
rs1280714	0.81[ASN][1000 genomes]
rs1280716	0.81[ASN][1000 genomes]
rs1354308	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1393859	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1395626	0.94[ASN][1000 genomes]
rs1415875	0.84[ASN][1000 genomes]
rs1507111	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1572594	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1827514	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1830662	0.81[ASN][1000 genomes]
rs1983141	0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2047828	0.81[ASN][1000 genomes]
rs2297805	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4094928	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4106094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715465	0.84[ASN][1000 genomes]
rs4715471	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4715472	0.82[EUR][1000 genomes]
rs4715473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs542639	0.88[ASN][1000 genomes]
rs58010645	0.97[ASN][1000 genomes]
rs62414317	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6459022	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906010	0.97[ASN][1000 genomes]
rs6907631	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs6909103	0.94[ASN][1000 genomes]
rs6916459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928097	0.84[ASN][1000 genomes]
rs6934405	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739195	0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7739425	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7747427	0.98[ASN][1000 genomes]
rs7759470	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7759660	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7770733	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7771107	0.84[ASN][1000 genomes]
rs7772650	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7773277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925053	0.95[ASN][1000 genomes]
rs925054	0.97[ASN][1000 genomes]
rs9296765	0.94[ASN][1000 genomes]
rs9296767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370324	0.81[ASN][1000 genomes]
rs9464125	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9464131	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474954	0.94[ASN][1000 genomes]
rs9474955	0.89[CHB][hapmap]
rs9474956	0.88[CHB][hapmap]
rs9474975	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9474976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474981	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474984	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474985	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962307	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs981683	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9918378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54595000-54595800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:54595400-54595800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54595400-54595800	Enhancers	NHEK	skin
4	chr6:54595600-54599800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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