Variant report

Variant	rs200983
Chromosome Location	chr6:27830326-27830327
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	chr6:26171577..26173697-chr6:27830155..27831800,2	MCF-7	breast:
2	chr6:27829699..27832078-chr8:101028376..101031173,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs12174918	0.93[ASN][1000 genomes]
rs13194781	0.88[EUR][1000 genomes]
rs13195728	0.85[EUR][1000 genomes]
rs13199649	0.86[EUR][1000 genomes]
rs13199772	0.88[EUR][1000 genomes]
rs13199906	0.88[EUR][1000 genomes]
rs13212651	0.88[EUR][1000 genomes]
rs13216117	0.85[EUR][1000 genomes]
rs13218875	0.80[EUR][1000 genomes]
rs169287	0.87[ASN][1000 genomes]
rs175597	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695758	0.88[EUR][1000 genomes]
rs17751184	0.85[EUR][1000 genomes]
rs17763089	0.88[EUR][1000 genomes]
rs183225	0.85[ASN][1000 genomes]
rs188015	0.83[EUR][1000 genomes]
rs200466	0.85[ASN][1000 genomes]
rs200469	0.83[ASN][1000 genomes]
rs200471	0.85[ASN][1000 genomes]
rs200473	0.85[ASN][1000 genomes]
rs200478	0.85[ASN][1000 genomes]
rs200479	0.85[ASN][1000 genomes]
rs200481	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200482	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200483	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200484	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200485	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200488	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200489	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200490	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200493	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200497	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200498	0.95[ASN][1000 genomes]
rs200499	0.93[ASN][1000 genomes]
rs200501	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200949	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200950	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200952	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200953	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200954	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200964	0.87[ASN][1000 genomes]
rs200965	0.89[ASN][1000 genomes]
rs200966	0.87[ASN][1000 genomes]
rs200968	0.89[ASN][1000 genomes]
rs200973	0.87[ASN][1000 genomes]
rs200974	0.89[ASN][1000 genomes]
rs200975	0.80[ASN][1000 genomes]
rs200976	0.87[ASN][1000 genomes]
rs200977	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200979	0.89[ASN][1000 genomes]
rs200980	0.89[ASN][1000 genomes]
rs200981	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200989	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200992	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200995	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200996	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201002	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277104	0.98[ASN][1000 genomes]
rs2394001	0.93[ASN][1000 genomes]
rs2747054	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28360499	0.83[EUR][1000 genomes]
rs34194357	0.88[EUR][1000 genomes]
rs34295134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34706883	0.85[EUR][1000 genomes]
rs34718920	0.85[EUR][1000 genomes]
rs34788973	0.85[EUR][1000 genomes]
rs35819751	0.88[EUR][1000 genomes]
rs36101351	0.85[EUR][1000 genomes]
rs36108923	1.00[ASN][1000 genomes]
rs36116761	0.88[EUR][1000 genomes]
rs370155	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs390764	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401754	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401763	0.95[ASN][1000 genomes]
rs45509595	0.88[EUR][1000 genomes]
rs4713122	0.93[ASN][1000 genomes]
rs4713124	0.93[ASN][1000 genomes]
rs4713127	0.93[ASN][1000 genomes]
rs483143	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs493161	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494887	0.89[ASN][1000 genomes]
rs557042	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56870390	1.00[ASN][1000 genomes]
rs59015666	0.93[ASN][1000 genomes]
rs61742093	0.85[EUR][1000 genomes]
rs666846	0.85[ASN][1000 genomes]
rs66868086	0.88[EUR][1000 genomes]
rs67040724	0.85[EUR][1000 genomes]
rs67101035	0.85[EUR][1000 genomes]
rs71559050	0.85[EUR][1000 genomes]
rs71559054	0.85[EUR][1000 genomes]
rs9348779	0.95[ASN][1000 genomes]
rs9357052	0.93[ASN][1000 genomes]
rs9368531	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368534	0.98[ASN][1000 genomes]
rs9368535	0.95[ASN][1000 genomes]
rs9368536	0.95[ASN][1000 genomes]
rs9380018	0.91[ASN][1000 genomes]
rs9380026	0.93[ASN][1000 genomes]
rs9393858	0.98[ASN][1000 genomes]
rs9393862	0.93[ASN][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	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	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
3	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
4	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
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200983	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200983	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200983	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27808000-27831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:27808200-27830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:27822800-27831800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:27824000-27831800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:27829000-27831800	Weak transcription	Right Atrium	heart
6	chr6:27830000-27830400	Enhancers	GM12878-XiMat	blood
7	chr6:27830000-27831000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:27830000-27831000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:27830000-27831200	Enhancers	HepG2	liver
10	chr6:27830000-27831800	Weak transcription	Dnd41	blood
11	chr6:27830200-27830400	Enhancers	K562	blood
12	chr6:27830200-27830600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:27830200-27830800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:27830200-27831400	Enhancers	Hela-S3	cervix
15	chr6:27830200-27831600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:27830200-27831600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:27830200-27831800	Weak transcription	Primary B cells from cord blood	blood

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