Variant report

Variant	rs11679518
Chromosome Location	chr2:48517552-48517553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48514433..48519005-chr2:48519179..48522844,4	K562	blood:
2	chr2:48513964..48516198-chr2:48516767..48519055,2	MCF-7	breast:
3	chr2:48517525..48519074-chr2:48557962..48560768,2	K562	blood:
4	chr2:48515255..48518583-chr2:48539283..48541492,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10195717	1.00[CEU][hapmap]
rs11674217	0.88[CEU][hapmap]
rs11674317	0.80[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11676925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11677205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11678934	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes]
rs11680657	0.83[EUR][1000 genomes]
rs11680968	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11682838	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11683202	0.85[TSI][hapmap]
rs11687276	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11687401	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11687461	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11687851	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11689285	0.88[CEU][hapmap]
rs11691302	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11691407	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11692537	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs11694094	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11694955	1.00[AFR][1000 genomes]
rs11695923	0.83[EUR][1000 genomes]
rs13398456	1.00[CEU][hapmap]
rs17325209	0.84[EUR][1000 genomes]
rs17396793	0.80[CEU][hapmap]
rs17397094	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17397449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs2014675	0.83[EUR][1000 genomes]
rs2937	0.88[CEU][hapmap]
rs4364065	1.00[AFR][1000 genomes]
rs4530419	0.80[CEU][hapmap]
rs6733558	0.80[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs6747738	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7583719	0.80[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs952468	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11679518	MSH6	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48506000-48539000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:48514000-48519400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:48514200-48517600	Weak transcription	K562	blood
4	chr2:48515800-48519200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:48516200-48519400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:48516800-48522200	Weak transcription	Primary B cells from peripheral blood	blood

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