Variant report

Variant	rs12526754
Chromosome Location	chr6:133060195-133060196
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	chr6:133053489..133056295-chr6:133060102..133062322,2	K562	blood:

Variant related genes	Relation type
ENSG00000093134	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10872396	0.81[AMR][1000 genomes]
rs11752749	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1883613	0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1883617	0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2267952	0.83[JPT][hapmap]
rs2294758	0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2294759	0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2300078	0.86[JPT][hapmap]
rs2300079	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2327276	0.81[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs3756974	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3813349	0.87[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3901670	0.86[JPT][hapmap]
rs4897614	0.82[CHB][hapmap];0.92[ASN][1000 genomes]
rs56739181	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6569836	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs6569837	0.81[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569839	0.82[CHB][hapmap];0.94[ASN][1000 genomes]
rs6569841	0.94[ASN][1000 genomes]
rs6569842	0.94[ASN][1000 genomes]
rs6569843	0.87[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899338	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6925157	0.89[JPT][hapmap]
rs6935500	0.88[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6937989	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6938188	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6942306	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs764263	0.99[ASN][1000 genomes]
rs7752016	0.80[JPT][hapmap]
rs7770949	0.94[ASN][1000 genomes]
rs9493423	0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9493425	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9493426	0.86[JPT][hapmap]
rs960711	0.88[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[ASN][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv965662	chr6:133058111-133063853	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12526754	VNN1	cis	Whole Blood	GTEx
rs12526754	VNN2	cis	Whole Blood	GTEx
rs12526754	VNN3	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133044400-133066200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:133055200-133064800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:133056800-133067400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:133057600-133069200	Weak transcription	GM12878-XiMat	blood
5	chr6:133058400-133061800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:133058400-133064800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:133058400-133070400	Weak transcription	Liver	Liver
8	chr6:133058600-133062600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:133058800-133061000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:133058800-133067600	Weak transcription	Placenta	Placenta
11	chr6:133059000-133060800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:133059800-133060400	Enhancers	Stomach Mucosa	stomach

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