Variant report

Variant	rs13193295
Chromosome Location	chr6:28003228-28003229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27999731..28002112-chr6:28002900..28005116,2	MCF-7	breast:
2	chr6:28001746..28003374-chr6:28020491..28023392,2	K562	blood:

Variant related genes	Relation type
ENSG00000182477	Chromatin interaction
ENSG00000217315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13194781	0.89[EUR][1000 genomes]
rs13195728	0.85[EUR][1000 genomes]
rs13199649	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13199772	0.89[EUR][1000 genomes]
rs13199906	0.89[EUR][1000 genomes]
rs13200214	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13212651	0.89[EUR][1000 genomes]
rs13216117	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13218875	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs149943	0.83[EUR][1000 genomes]
rs156743	0.83[EUR][1000 genomes]
rs17695758	0.89[EUR][1000 genomes]
rs17751184	0.85[EUR][1000 genomes]
rs17763089	0.89[EUR][1000 genomes]
rs28360499	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34194357	0.89[EUR][1000 genomes]
rs34706883	0.85[EUR][1000 genomes]
rs34718920	0.85[EUR][1000 genomes]
rs34788973	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35819751	0.89[EUR][1000 genomes]
rs36101351	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36116761	0.89[EUR][1000 genomes]
rs45509595	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61742093	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66868086	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67040724	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67101035	0.85[EUR][1000 genomes]
rs71537572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559050	0.85[EUR][1000 genomes]
rs71559054	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1817841	chr6:27984907-28007435	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13193295	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13193295	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13193295	AL022393.7	cis	Muscle Skeletal	GTEx
rs13193295	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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