Variant report

Variant	rs2747467
Chromosome Location	chr6:29659124-29659125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs2107203	0.94[AFR][1000 genomes]
rs2158290	0.94[AFR][1000 genomes]
rs2535274	0.84[AFR][1000 genomes]
rs2535275	0.84[AFR][1000 genomes]
rs2747427	0.81[AFR][1000 genomes]
rs2747428	0.81[AFR][1000 genomes]
rs2747429	0.81[AFR][1000 genomes]
rs2747430	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747431	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2747460	0.83[AFR][1000 genomes]
rs2907897	0.84[AFR][1000 genomes]
rs3094729	0.90[AFR][1000 genomes]
rs3094732	0.94[AFR][1000 genomes]
rs3094734	0.94[AFR][1000 genomes]
rs3116800	0.91[AFR][1000 genomes]
rs3116802	0.89[AFR][1000 genomes]
rs3116803	0.94[AFR][1000 genomes]
rs3116804	0.94[AFR][1000 genomes]
rs3116812	0.80[ASN][1000 genomes]
rs3116814	0.84[AFR][1000 genomes]
rs3117301	0.84[AFR][1000 genomes]
rs3129033	0.84[AFR][1000 genomes]
rs3129035	0.84[AFR][1000 genomes]
rs3129037	0.87[AFR][1000 genomes]
rs3129042	0.94[AFR][1000 genomes]
rs3129044	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129047	0.94[AFR][1000 genomes]
rs3129048	0.92[AFR][1000 genomes]
rs3129055	0.94[AFR][1000 genomes]
rs3129056	0.94[AFR][1000 genomes]
rs3129061	0.94[AFR][1000 genomes]
rs3129062	0.82[AFR][1000 genomes]
rs3129065	0.94[AFR][1000 genomes]
rs3129066	0.94[AFR][1000 genomes]
rs3129067	0.94[AFR][1000 genomes]
rs3129070	0.94[AFR][1000 genomes]
rs3129072	0.94[AFR][1000 genomes]
rs3129082	0.88[AFR][1000 genomes]
rs3129086	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3131866	0.94[AFR][1000 genomes]
rs3131868	0.91[AFR][1000 genomes]
rs3131870	0.94[AFR][1000 genomes]
rs3131871	0.94[AFR][1000 genomes]
rs3131872	0.94[AFR][1000 genomes]
rs3131873	0.94[AFR][1000 genomes]
rs3131874	0.94[AFR][1000 genomes]
rs3131884	0.88[AFR][1000 genomes]
rs3131890	0.82[AFR][1000 genomes]
rs365052	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs387640	0.82[AFR][1000 genomes]
rs387642	0.82[AFR][1000 genomes]
rs396660	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs416568	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs417764	0.81[AFR][1000 genomes]
rs444189	0.82[ASN][1000 genomes]
rs445150	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9258048	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9258051	0.81[ASN][1000 genomes]
rs9258074	0.94[AFR][1000 genomes]
rs9258078	0.94[AFR][1000 genomes]
rs9258079	0.94[AFR][1000 genomes]
rs9258083	0.94[AFR][1000 genomes]
rs9258087	0.94[AFR][1000 genomes]
rs9258088	0.94[AFR][1000 genomes]
rs9258103	0.93[AFR][1000 genomes]
rs9258104	0.84[AFR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1840790	chr6:29658864-29669830	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2747467	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2747467	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2747467	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs2747467	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29648800-29662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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