Variant report

Variant	rs2221824
Chromosome Location	chr6:23877024-23877025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11756885	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355458	0.84[EUR][1000 genomes]
rs1355459	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17299436	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17299457	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036886	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2036887	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036888	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2036889	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4327688	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58398055	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900723	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908183	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6921319	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741044	0.95[EUR][1000 genomes]
rs7752738	0.91[EUR][1000 genomes]
rs9460939	0.82[EUR][1000 genomes]
rs9466937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs9466949	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9466955	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9466956	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9466977	0.82[EUR][1000 genomes]
rs9466978	0.85[EUR][1000 genomes]
rs953377	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs953378	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3442143	chr6:23686264-23978363	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv883479	chr6:23804221-24090497	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1034848	chr6:23857972-23976276	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv524433	chr6:23858932-23978607	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2221824	BTN3A1	cis	parietal	SCAN
rs2221824	BTN3A2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:23870400-23877200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:23873600-23881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:23876600-23877400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:23877000-23877200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links