Variant report

Variant	rs34724414
Chromosome Location	chr6:28619353-28619354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1233579	0.87[EUR][1000 genomes]
rs1233580	0.87[EUR][1000 genomes]
rs1233581	0.87[EUR][1000 genomes]
rs1233583	0.87[EUR][1000 genomes]
rs1233593	0.87[EUR][1000 genomes]
rs1233594	0.87[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.87[EUR][1000 genomes]
rs1311911	0.85[EUR][1000 genomes]
rs1311912	0.87[EUR][1000 genomes]
rs1311913	0.87[EUR][1000 genomes]
rs13191038	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13194504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1742743	0.85[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35044849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35243068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4947336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6456835	0.89[EUR][1000 genomes]
rs6908726	0.93[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs9257133	0.87[EUR][1000 genomes]
rs9257136	0.87[EUR][1000 genomes]
rs9257137	0.87[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9257167	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9393926	0.93[EUR][1000 genomes]
rs9393929	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34724414	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34724414	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34724414	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28616800-28625200	Weak transcription	Colonic Mucosa	Colon
2	chr6:28617200-28624600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28617200-28624800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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