Variant report

Variant	rs493161
Chromosome Location	chr6:27850714-27850715
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs12174918	0.86[ASN][1000 genomes]
rs13194781	0.90[EUR][1000 genomes]
rs13195728	0.86[EUR][1000 genomes]
rs13199649	0.88[EUR][1000 genomes]
rs13199772	0.90[EUR][1000 genomes]
rs13199906	0.90[EUR][1000 genomes]
rs13212651	0.90[EUR][1000 genomes]
rs13216117	0.86[EUR][1000 genomes]
rs13218875	0.81[EUR][1000 genomes]
rs169287	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs175597	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17695758	0.90[EUR][1000 genomes]
rs17751184	0.86[EUR][1000 genomes]
rs17763089	0.90[EUR][1000 genomes]
rs188015	0.84[EUR][1000 genomes]
rs200481	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200482	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200483	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200484	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200485	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200488	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs200489	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200490	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200493	0.92[EUR][1000 genomes]
rs200497	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200498	0.88[ASN][1000 genomes]
rs200499	0.86[ASN][1000 genomes]
rs200501	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200948	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200949	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200950	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200952	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200953	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200954	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200964	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200965	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200966	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200968	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200973	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200974	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200975	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs200976	0.93[ASN][1000 genomes]
rs200977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200979	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200980	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs200981	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200983	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200989	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200990	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200992	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200995	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200996	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs201002	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277104	0.91[ASN][1000 genomes]
rs2394001	0.86[ASN][1000 genomes]
rs2747054	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28360499	0.85[EUR][1000 genomes]
rs34194357	0.90[EUR][1000 genomes]
rs34295134	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34706883	0.86[EUR][1000 genomes]
rs34718920	0.86[EUR][1000 genomes]
rs34788973	0.86[EUR][1000 genomes]
rs35819751	0.90[EUR][1000 genomes]
rs36101351	0.86[EUR][1000 genomes]
rs36108923	0.93[ASN][1000 genomes]
rs36116761	0.90[EUR][1000 genomes]
rs370155	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs390764	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs401754	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs401763	0.88[ASN][1000 genomes]
rs45509595	0.90[EUR][1000 genomes]
rs4713122	0.86[ASN][1000 genomes]
rs4713124	0.86[ASN][1000 genomes]
rs4713127	1.00[ASN][1000 genomes]
rs483143	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494887	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs557042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56870390	0.93[ASN][1000 genomes]
rs59015666	0.86[ASN][1000 genomes]
rs61742093	0.86[EUR][1000 genomes]
rs66868086	0.90[EUR][1000 genomes]
rs67040724	0.86[EUR][1000 genomes]
rs67101035	0.86[EUR][1000 genomes]
rs71559050	0.86[EUR][1000 genomes]
rs71559054	0.86[EUR][1000 genomes]
rs9348779	0.98[ASN][1000 genomes]
rs9357052	1.00[ASN][1000 genomes]
rs9368531	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368534	0.91[ASN][1000 genomes]
rs9368535	0.98[ASN][1000 genomes]
rs9368536	0.98[ASN][1000 genomes]
rs9380018	0.84[ASN][1000 genomes]
rs9380026	1.00[ASN][1000 genomes]
rs9393858	0.91[ASN][1000 genomes]
rs9393862	1.00[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	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
7	nsv601209	chr6:27849676-27869321	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	194 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs493161	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs493161	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs493161	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27842200-27857000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:27842600-27855600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27842800-27855600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:27848000-27855800	Weak transcription	Dnd41	blood
5	chr6:27848200-27855400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:27848200-27855800	Weak transcription	K562	blood
7	chr6:27848200-27857000	Weak transcription	Thymus	Thymus
8	chr6:27849400-27850800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:27849400-27851200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:27849800-27850800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:27850000-27850800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:27850200-27855600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:27850400-27851000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:27850600-27851000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:27850600-27851000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:27850600-27851000	Weak transcription	Placenta	Placenta
17	chr6:27850600-27857200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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