Variant report

Variant	rs200468
Chromosome Location	chr6:27757855-27757856
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27753086..27755536-chr6:27756533..27760305,3	MCF-7	breast:
2	chr6:27744586..27748272-chr6:27756903..27759108,3	MCF-7	breast:
3	chr6:27154579..27158488-chr6:27757538..27761648,4	MCF-7	breast:
4	chr6:27114006..27117036-chr6:27757765..27761399,4	MCF-7	breast:
5	chr6:27109661..27117801-chr6:27755492..27760111,8	K562	blood:
6	chr6:27559085..27561066-chr6:27755940..27758239,2	K562	blood:
7	chr6:27154554..27158026-chr6:27757603..27761465,4	K562	blood:
8	chr6:27113525..27116337-chr6:27757197..27759712,2	MCF-7	breast:
9	chr6:27112343..27120362-chr6:27757252..27765476,17	K562	blood:
10	chr6:27519736..27522304-chr6:27757079..27759597,2	MCF-7	breast:

No data

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

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10214440	0.85[ASN][1000 genomes]
rs10484401	0.92[ASN][1000 genomes]
rs13211701	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs169262	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985099	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200474	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200475	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200476	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2056925	0.84[ASN][1000 genomes]
rs2092075	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2179094	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2179095	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2394000	0.81[ASN][1000 genomes]
rs2394002	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2893929	0.92[ASN][1000 genomes]
rs2893930	0.89[ASN][1000 genomes]
rs2893931	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35069907	0.90[ASN][1000 genomes]
rs35957409	0.91[ASN][1000 genomes]
rs4140646	0.89[ASN][1000 genomes]
rs4711163	0.95[ASN][1000 genomes]
rs4713121	0.97[ASN][1000 genomes]
rs6901520	0.90[ASN][1000 genomes]
rs6902689	0.88[ASN][1000 genomes]
rs6914924	0.90[ASN][1000 genomes]
rs6922574	0.85[ASN][1000 genomes]
rs6930992	0.89[ASN][1000 genomes]
rs6940116	0.80[EUR][1000 genomes]
rs742046	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs742047	0.92[ASN][1000 genomes]
rs760587	0.92[ASN][1000 genomes]
rs7756968	0.92[ASN][1000 genomes]
rs7759217	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7760523	0.91[ASN][1000 genomes]
rs7772027	0.80[ASN][1000 genomes]
rs7773070	0.97[ASN][1000 genomes]
rs7776351	0.97[ASN][1000 genomes]
rs9283880	0.91[ASN][1000 genomes]
rs9283881	0.91[ASN][1000 genomes]
rs9283882	0.91[ASN][1000 genomes]
rs9283883	0.91[ASN][1000 genomes]
rs9295740	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9295742	0.85[ASN][1000 genomes]
rs9295743	0.90[ASN][1000 genomes]
rs9295746	0.92[ASN][1000 genomes]
rs9348774	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9348775	0.85[ASN][1000 genomes]
rs9357045	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9366700	0.85[ASN][1000 genomes]
rs9366702	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9368528	0.81[ASN][1000 genomes]
rs9368529	0.81[ASN][1000 genomes]
rs9368530	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9380010	0.81[ASN][1000 genomes]
rs9380012	0.81[ASN][1000 genomes]
rs9393847	0.81[ASN][1000 genomes]
rs9393848	0.81[ASN][1000 genomes]
rs9461401	0.85[ASN][1000 genomes]
rs9461405	0.91[ASN][1000 genomes]
rs9461406	0.86[ASN][1000 genomes]
rs9468200	0.81[ASN][1000 genomes]
rs9468201	0.81[ASN][1000 genomes]
rs9468203	0.81[ASN][1000 genomes]
rs9468204	0.81[ASN][1000 genomes]
rs9468206	0.81[ASN][1000 genomes]
rs9468214	0.90[ASN][1000 genomes]
rs9468217	0.92[ASN][1000 genomes]
rs9468219	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9468220	0.92[ASN][1000 genomes]
rs9468223	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9468229	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[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
rs200468	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200468	AL022393.7	cis	Muscle Skeletal	GTEx
rs200468	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27751600-27759200	Weak transcription	Colonic Mucosa	Colon
2	chr6:27753800-27759000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27754000-27759200	Weak transcription	HepG2	liver
4	chr6:27754200-27759000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:27754600-27759000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:27755200-27759200	Weak transcription	K562	blood

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