Variant report

Variant	rs6539242
Chromosome Location	chr12:106334180-106334181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106327450..106330150-chr12:106332970..106335467,4	MCF-7	breast:
2	chr12:106332698..106335575-chr12:106336586..106338838,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10507207	0.85[EUR][1000 genomes]
rs10861535	0.82[EUR][1000 genomes]
rs11112808	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112810	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112812	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112815	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11608722	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611601	0.85[EUR][1000 genomes]
rs11833383	0.92[AFR][1000 genomes]
rs11837217	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837987	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297788	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425164	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426791	0.85[EUR][1000 genomes]
rs12426802	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582103	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810562	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814823	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815201	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12816747	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12818417	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832619	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12833614	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344566	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344567	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1345543	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1362980	0.85[EUR][1000 genomes]
rs1362981	0.85[EUR][1000 genomes]
rs1421454	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421457	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421458	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421459	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895105	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895106	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2032772	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2080755	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539238	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539239	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539240	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539241	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300069	0.85[EUR][1000 genomes]
rs7312545	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7953002	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953243	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955474	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7958273	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960459	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961513	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965501	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969437	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971140	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973513	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973846	0.85[EUR][1000 genomes]
rs7976523	0.85[EUR][1000 genomes]
rs9630290	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106325400-106336600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:106325600-106335200	Enhancers	HMEC	breast
3	chr12:106327200-106335000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:106328200-106339200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:106328600-106335000	Enhancers	NHEK	skin
6	chr12:106331000-106337200	Weak transcription	HSMM	muscle
7	chr12:106331000-106337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:106331800-106334800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:106332200-106337200	Weak transcription	HSMMtube	muscle
10	chr12:106334000-106337400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:106334000-106339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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