Variant report

Variant	rs9468229
Chromosome Location	chr6:27750086-27750087
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	chr6:27750078..27752757-chr6:27753756..27756420,3	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10214440	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10484401	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139226	0.82[EUR][1000 genomes]
rs13211701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215072	0.81[EUR][1000 genomes]
rs169262	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1985099	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200468	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs200474	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs200475	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs200476	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2056925	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2092075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179094	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2179095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394000	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394002	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2893929	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893930	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2893931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34752872	0.89[EUR][1000 genomes]
rs35069907	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35957409	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4140646	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711163	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713118	0.82[EUR][1000 genomes]
rs4713121	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6901520	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902689	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914924	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922574	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6930992	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs742046	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742047	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs760587	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756968	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759217	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760523	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7772027	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7773070	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776351	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9283880	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283881	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283882	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283883	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295740	0.81[ASN][1000 genomes]
rs9295742	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295743	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295746	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348774	0.81[ASN][1000 genomes]
rs9348775	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357045	0.81[ASN][1000 genomes]
rs9366700	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366702	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368528	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368529	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368530	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380010	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380011	0.89[EUR][1000 genomes]
rs9380012	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393847	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393848	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461401	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461405	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461406	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468195	0.82[EUR][1000 genomes]
rs9468200	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468201	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468203	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468204	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468206	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9468214	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468217	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468219	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468220	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468223	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv981120	chr6:27746371-27751747	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
8	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9468229	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9468229	OR2B8P	cis	Thyroid	GTEx
rs9468229	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468229	AL022393.7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27745600-27753200	Weak transcription	HepG2	liver
2	chr6:27748800-27754600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr6:27750000-27750800	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr6:27750000-27751200	Enhancers	Fetal Intestine Small	intestine
5	chr6:27750000-27751600	Enhancers	K562	blood

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