Variant report

Variant	rs12189640
Chromosome Location	chr6:27474657-27474658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27472071..27474860-chr6:27486354..27488722,3	K562	blood:
2	chr6:27471243..27473118-chr6:27473124..27475261,2	K562	blood:
3	chr6:27472621..27475271-chr6:27477554..27480516,2	MCF-7	breast:
4	chr6:27112845..27117785-chr6:27470908..27475349,7	K562	blood:
5	chr6:27474407..27478375-chr6:27478575..27482330,4	K562	blood:
6	chr6:27469947..27474974-chr6:27485508..27488698,9	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10456051	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];0.98[EUR][1000 genomes]
rs10456355	0.81[AMR][1000 genomes]
rs12191373	1.00[CEU][hapmap]
rs12191414	0.85[CEU][hapmap]
rs12191649	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12192560	0.93[AMR][1000 genomes]
rs12193557	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12194341	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12194842	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];0.81[EUR][1000 genomes]
rs12194893	1.00[GIH][hapmap]
rs12195783	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]
rs12196452	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs12196970	0.86[AMR][1000 genomes]
rs12199685	1.00[AMR][1000 genomes]
rs12199806	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12202956	1.00[AMR][1000 genomes]
rs12204953	1.00[AMR][1000 genomes]
rs12205044	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12209174	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12209905	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12211931	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12212348	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs12212389	1.00[AMR][1000 genomes]
rs12212632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12213471	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12213533	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs12215289	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12215353	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12215386	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12215878	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs12374607	1.00[AMR][1000 genomes]
rs12374649	1.00[AMR][1000 genomes]
rs56099947	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57075114	0.88[EUR][1000 genomes]
rs60888769	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62617138	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71546544	0.84[AMR][1000 genomes]
rs72839468	0.86[AMR][1000 genomes]
rs72839469	0.86[AMR][1000 genomes]
rs72839470	0.86[AMR][1000 genomes]
rs72839471	1.00[AMR][1000 genomes]
rs72839474	1.00[AMR][1000 genomes]
rs72839479	1.00[AMR][1000 genomes]
rs72841397	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72841398	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72841399	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72841400	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72843151	1.00[AMR][1000 genomes]
rs72843177	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72843191	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72845006	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72845008	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72845011	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72845012	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72845025	0.84[AMR][1000 genomes]
rs72845027	0.84[AMR][1000 genomes]
rs72845028	0.84[AMR][1000 genomes]
rs72845030	0.84[AMR][1000 genomes]
rs72845031	0.84[AMR][1000 genomes]
rs72845042	0.84[AMR][1000 genomes]
rs72845044	0.84[AMR][1000 genomes]
rs72845050	0.84[AMR][1000 genomes]
rs72845208	0.93[AMR][1000 genomes]
rs72845232	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9348763	0.86[AMR][1000 genomes]
rs9368509	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9379975	0.86[AMR][1000 genomes]
rs9393814	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27471600-27479800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:27473200-27475200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:27473800-27475400	Enhancers	Hela-S3	cervix
4	chr6:27474200-27474800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:27474200-27474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:27474200-27480000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:27474600-27474800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27474600-27474800	Enhancers	A549	lung
9	chr6:27474600-27474800	Flanking Active TSS	K562	blood
10	chr6:27474600-27475000	Flanking Active TSS	HepG2	liver

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