Variant report

Variant	rs3996937
Chromosome Location	chr6:56905631-56905632
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56877566..56879114-chr6:56904825..56906566,2	MCF-7	breast:
2	chr6:56834918..56837868-chr6:56903962..56906582,2	MCF-7	breast:
3	chr6:56905300..56907773-chr6:56908379..56910972,2	K562	blood:
4	chr6:56820096..56821611-chr6:56902889..56905830,2	K562	blood:
5	chr6:56818651..56821611-chr6:56903596..56905830,2	K562	blood:
6	chr6:56900127..56902056-chr6:56904004..56905904,2	K562	blood:

Variant related genes	Relation type
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1157713	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190416	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190434	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192711	0.82[ASN][1000 genomes]
rs12211611	0.82[ASN][1000 genomes]
rs1901382	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2100305	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273921	0.82[ASN][1000 genomes]
rs3734738	0.82[ASN][1000 genomes]
rs3778515	0.82[ASN][1000 genomes]
rs3996929	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3996933	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715646	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913707	0.93[EUR][1000 genomes]
rs6926980	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6928715	0.82[ASN][1000 genomes]
rs6929783	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936472	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7743855	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7744824	0.80[ASN][1000 genomes]
rs7753537	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7753927	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763570	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8180538	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9349843	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9367704	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367708	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370564	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370565	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382689	0.82[ASN][1000 genomes]
rs9396259	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs952647	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9885757	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1026524	chr6:56902544-56951703	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3996937	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3996937	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56905000-56906000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:56905600-56905800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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