Variant report

Variant	rs28360499
Chromosome Location	chr6:27945396-27945397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27932549..27935599-chr6:27943832..27947196,3	K562	blood:

Variant related genes	Relation type
ENSG00000214374	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs13193295	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13194781	0.95[EUR][1000 genomes]
rs13195728	0.91[EUR][1000 genomes]
rs13199649	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13199772	0.95[EUR][1000 genomes]
rs13199906	0.95[EUR][1000 genomes]
rs13200214	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13212651	0.95[EUR][1000 genomes]
rs13216117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13218875	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs175597	0.85[EUR][1000 genomes]
rs17695758	0.95[EUR][1000 genomes]
rs17750747	0.84[EUR][1000 genomes]
rs17751184	0.91[EUR][1000 genomes]
rs17763089	0.95[EUR][1000 genomes]
rs188015	0.82[EUR][1000 genomes]
rs200481	0.81[EUR][1000 genomes]
rs200483	0.81[EUR][1000 genomes]
rs200485	0.81[EUR][1000 genomes]
rs200489	0.81[EUR][1000 genomes]
rs200501	0.81[EUR][1000 genomes]
rs200948	0.85[EUR][1000 genomes]
rs200950	0.85[EUR][1000 genomes]
rs200952	0.85[EUR][1000 genomes]
rs200953	0.83[EUR][1000 genomes]
rs200954	0.85[EUR][1000 genomes]
rs200977	0.85[EUR][1000 genomes]
rs200981	0.83[EUR][1000 genomes]
rs200983	0.83[EUR][1000 genomes]
rs200989	0.85[EUR][1000 genomes]
rs200990	0.83[EUR][1000 genomes]
rs200995	0.85[EUR][1000 genomes]
rs200996	0.83[EUR][1000 genomes]
rs201002	0.83[EUR][1000 genomes]
rs2747054	0.81[EUR][1000 genomes]
rs34194357	0.95[EUR][1000 genomes]
rs34295134	0.83[EUR][1000 genomes]
rs34706883	0.91[EUR][1000 genomes]
rs34718920	0.91[EUR][1000 genomes]
rs34788973	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35037868	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35501037	0.84[EUR][1000 genomes]
rs35819751	0.95[EUR][1000 genomes]
rs36101351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36116761	0.95[EUR][1000 genomes]
rs390764	0.81[EUR][1000 genomes]
rs401754	0.81[EUR][1000 genomes]
rs45509595	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs483143	0.83[EUR][1000 genomes]
rs493161	0.85[EUR][1000 genomes]
rs557042	0.85[EUR][1000 genomes]
rs61742093	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66868086	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67040724	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67101035	0.91[EUR][1000 genomes]
rs71537572	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71559050	0.91[EUR][1000 genomes]
rs71559054	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72847313	0.84[EUR][1000 genomes]
rs9368531	0.81[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	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28360499	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs28360499	AL022393.7	cis	Muscle Skeletal	GTEx
rs28360499	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs28360499	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27944800-27945400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:27944800-27945800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:27945200-27945800	Flanking Active TSS	K562	blood

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