Variant report

Variant	rs200476
Chromosome Location	chr6:27768348-27768349
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27098199..27102217-chr6:27766076..27771196,5	MCF-7	breast:
2	chr6:27763449..27765293-chr6:27766819..27768521,2	MCF-7	breast:
3	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10214440	0.82[ASN][1000 genomes]
rs10484401	0.90[ASN][1000 genomes]
rs13211701	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs169262	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985099	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200468	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200474	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200475	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056925	0.81[ASN][1000 genomes]
rs2092075	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2179094	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2179095	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2394002	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2893929	0.90[ASN][1000 genomes]
rs2893930	0.87[ASN][1000 genomes]
rs2893931	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35069907	0.88[ASN][1000 genomes]
rs35957409	0.87[ASN][1000 genomes]
rs4140646	0.87[ASN][1000 genomes]
rs4711163	0.91[ASN][1000 genomes]
rs4713121	0.92[ASN][1000 genomes]
rs6901520	0.86[ASN][1000 genomes]
rs6902689	0.84[ASN][1000 genomes]
rs6914924	0.86[ASN][1000 genomes]
rs6922574	0.82[ASN][1000 genomes]
rs6930992	0.85[ASN][1000 genomes]
rs742046	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs742047	0.90[ASN][1000 genomes]
rs760587	0.90[ASN][1000 genomes]
rs7756968	0.90[ASN][1000 genomes]
rs7759217	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7760523	0.87[ASN][1000 genomes]
rs7773070	0.92[ASN][1000 genomes]
rs7776351	0.92[ASN][1000 genomes]
rs9283880	0.87[ASN][1000 genomes]
rs9283881	0.87[ASN][1000 genomes]
rs9283882	0.87[ASN][1000 genomes]
rs9283883	0.87[ASN][1000 genomes]
rs9295742	0.82[ASN][1000 genomes]
rs9295743	0.88[ASN][1000 genomes]
rs9295746	0.90[ASN][1000 genomes]
rs9348774	0.80[EUR][1000 genomes]
rs9348775	0.82[ASN][1000 genomes]
rs9366700	0.82[ASN][1000 genomes]
rs9366702	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9368530	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9461401	0.82[ASN][1000 genomes]
rs9461405	0.87[ASN][1000 genomes]
rs9461406	0.83[ASN][1000 genomes]
rs9468214	0.86[ASN][1000 genomes]
rs9468217	0.88[ASN][1000 genomes]
rs9468219	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9468220	0.90[ASN][1000 genomes]
rs9468223	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9468229	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	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
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	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
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200476	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200476	AL022393.7	cis	Muscle Skeletal	GTEx
rs200476	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27761200-27768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:27761600-27768600	Weak transcription	NHEK	skin
3	chr6:27764400-27768400	Enhancers	K562	blood
4	chr6:27764400-27774200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:27764600-27768600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:27766600-27768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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