Variant report

Variant	rs4327688
Chromosome Location	chr6:23890877-23890878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:23879136..23881788-chr6:23889140..23891647,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11756885	0.90[EUR][1000 genomes]
rs1355458	0.83[EUR][1000 genomes]
rs1355459	0.90[EUR][1000 genomes]
rs17299436	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17299457	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2036888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036889	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2221824	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58398055	0.90[EUR][1000 genomes]
rs6900723	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6908183	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6921319	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7741044	0.91[EUR][1000 genomes]
rs7752738	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9460939	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9466937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs9466949	0.90[EUR][1000 genomes]
rs9466955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9466956	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9466977	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9466978	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs953378	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
6	nsv462657	chr6:23879940-23896587	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv601142	chr6:23879940-23896587	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2763541	chr6:23887115-23946559	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv470804	chr6:23890877-23946867	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4327688	BTN3A1	cis	parietal	SCAN
rs4327688	BTN3A2	cis	parietal	SCAN
rs4327688	HIST1H4G	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:23890600-23891400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:23890800-23891000	Active TSS	Liver	Liver
3	chr6:23890800-23891200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:23890800-23893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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