Variant report

Variant	rs6940959
Chromosome Location	chr6:133418773-133418774
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	chr6:133418545..133420592-chr6:133429051..133431256,2	MCF-7	breast:
2	chr6:133417078..133419913-chr6:133422627..133424632,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10457002	0.90[EUR][1000 genomes]
rs10457600	0.83[EUR][1000 genomes]
rs10457602	1.00[CEU][hapmap]
rs10457603	1.00[CEU][hapmap]
rs11154715	0.81[EUR][1000 genomes]
rs12154207	0.81[EUR][1000 genomes]
rs12191026	0.81[EUR][1000 genomes]
rs12192002	0.96[EUR][1000 genomes]
rs12192605	0.96[EUR][1000 genomes]
rs12193118	0.86[EUR][1000 genomes]
rs12196492	0.81[EUR][1000 genomes]
rs12198619	0.85[EUR][1000 genomes]
rs12199138	0.83[EUR][1000 genomes]
rs12199555	0.81[EUR][1000 genomes]
rs12199958	0.81[EUR][1000 genomes]
rs12200155	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12200393	0.81[EUR][1000 genomes]
rs12201315	1.00[CEU][hapmap]
rs12205139	0.91[EUR][1000 genomes]
rs12210216	0.81[EUR][1000 genomes]
rs12211999	0.81[EUR][1000 genomes]
rs12212715	0.90[EUR][1000 genomes]
rs12213350	0.83[EUR][1000 genomes]
rs12213452	0.83[EUR][1000 genomes]
rs12213690	0.81[EUR][1000 genomes]
rs12215217	0.83[EUR][1000 genomes]
rs28538690	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077767	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077768	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4257872	0.80[EUR][1000 genomes]
rs4273707	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273708	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57161827	0.94[EUR][1000 genomes]
rs58835706	0.90[EUR][1000 genomes]
rs59793266	0.81[EUR][1000 genomes]
rs62428563	0.82[EUR][1000 genomes]
rs62428596	0.81[EUR][1000 genomes]
rs62430562	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62430580	0.85[EUR][1000 genomes]
rs62430581	0.85[EUR][1000 genomes]
rs62430582	0.90[EUR][1000 genomes]
rs62430588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62430590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569863	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs6902225	0.86[EUR][1000 genomes]
rs6911954	0.90[EUR][1000 genomes]
rs6913444	0.82[EUR][1000 genomes]
rs6927627	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933214	0.87[EUR][1000 genomes]
rs6935070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6937029	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939899	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72557636	0.90[EUR][1000 genomes]
rs7738156	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7738592	0.95[EUR][1000 genomes]
rs7746390	0.81[EUR][1000 genomes]
rs7748926	0.82[EUR][1000 genomes]
rs7750218	0.82[EUR][1000 genomes]
rs7750279	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7750376	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7754486	1.00[CEU][hapmap]
rs7756171	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7756963	0.83[EUR][1000 genomes]
rs7761372	0.96[EUR][1000 genomes]
rs7767651	0.81[EUR][1000 genomes]
rs7770031	0.82[EUR][1000 genomes]
rs9321388	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9321389	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9483529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483535	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9483554	0.81[EUR][1000 genomes]
rs9493513	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9493514	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9493515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957183	0.82[EUR][1000 genomes]
rs975225	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv428154	chr6:133271975-133522803	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3445931	chr6:133347824-133434532	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv519475	chr6:133350936-133474673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6940959	HBS1L	cis	cerebellum	SCAN
rs6940959	HBS1L	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133410800-133420200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:133416200-133420800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:133416600-133420400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:133416800-133420000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:133417200-133422200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:133417200-133422600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:133417800-133418800	Enhancers	HMEC	breast
8	chr6:133417800-133419000	Enhancers	NHEK	skin
9	chr6:133418200-133418800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:133418200-133418800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:133418600-133421000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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