Variant report

Variant	rs16893533
Chromosome Location	chr6:27933709-27933710
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27932549..27935599-chr6:27943832..27947196,3	K562	blood:
2	chr6:27933640..27936048-chr6:27973424..27976149,2	K562	blood:

Variant related genes	Relation type
ENSG00000216629	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10046419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs10046424	0.83[ASN][1000 genomes]
rs12178430	0.83[ASN][1000 genomes]
rs12332927	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12333142	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1497525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497526	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1564442	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16893540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16893549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16893731	1.00[CHB][hapmap]
rs17763319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[LWK][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs17765402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs17767294	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1873213	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277103	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs3757186	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs6456803	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6900413	0.82[CHB][hapmap]
rs73386659	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73392694	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73394715	0.87[ASN][1000 genomes]
rs73394718	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295749	0.84[LWK][hapmap]
rs9295750	0.82[CHB][hapmap]
rs9461419	0.93[EUR][1000 genomes]
rs9461420	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9461425	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9468252	1.00[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9468254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468255	0.87[ASN][1000 genomes]
rs9468264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9885649	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][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	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
2	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
3	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
4	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
5	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16893533	ZC3HC1	trans	brain	seeQTL
rs16893533	MRPL23	trans	brain	seeQTL
rs16893533	KIAA0100	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27932600-27935800	Enhancers	Primary B cells from peripheral blood	blood

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