Variant report

Variant	rs6083406
Chromosome Location	chr20:24140069-24140070
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24139018..24140898-chr20:24143950..24146165,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-6	chr20:24139985-24141327	NONHSAT079102

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12373871	1.00[ASN][1000 genomes]
rs28778436	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282312	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282314	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41282316	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55739770	0.86[EUR][1000 genomes]
rs55771985	0.83[EUR][1000 genomes]
rs56104572	0.83[EUR][1000 genomes]
rs59054030	0.83[EUR][1000 genomes]
rs59561448	0.83[EUR][1000 genomes]
rs6049548	0.90[EUR][1000 genomes]
rs6049555	0.83[EUR][1000 genomes]
rs6049556	0.83[EUR][1000 genomes]
rs6076190	0.83[EUR][1000 genomes]
rs6076194	0.83[EUR][1000 genomes]
rs6076195	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076200	1.00[ASN][1000 genomes]
rs6076205	0.86[EUR][1000 genomes]
rs6076206	1.00[ASN][1000 genomes]
rs6076214	0.83[EUR][1000 genomes]
rs6083388	0.83[EUR][1000 genomes]
rs6083390	0.83[EUR][1000 genomes]
rs6083391	0.83[EUR][1000 genomes]
rs6083398	0.83[EUR][1000 genomes]
rs6083400	0.83[EUR][1000 genomes]
rs6083404	0.86[EUR][1000 genomes]
rs6083408	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083409	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083424	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083432	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083433	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083438	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083439	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083440	1.00[ASN][1000 genomes]
rs6083441	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083449	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083452	0.86[EUR][1000 genomes]
rs6083463	0.83[EUR][1000 genomes]
rs6083464	0.83[EUR][1000 genomes]
rs6083465	0.83[EUR][1000 genomes]
rs6083467	0.83[EUR][1000 genomes]
rs6106813	0.83[EUR][1000 genomes]
rs73329997	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73333779	0.83[EUR][1000 genomes]
rs73335617	0.83[EUR][1000 genomes]
rs73337581	1.00[ASN][1000 genomes]
rs7354351	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962527	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24134400-24146800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24139200-24140800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr20:24139200-24140800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr20:24140000-24140600	Enhancers	Fetal Muscle Trunk	muscle
5	chr20:24140000-24140800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links