Variant report

Variant	rs9388953
Chromosome Location	chr6:132297509-132297510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000227220	Chromatin interaction
ENSG00000197594	Chromatin interaction
ENSG00000079931	Chromatin interaction
ENSG00000118523	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1475723	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1813069	0.84[AFR][1000 genomes]
rs1930995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1930996	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7767139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928505	0.89[LWK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs9483364	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9483365	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493153	0.96[ASN][1000 genomes]
rs9493157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9493160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470861	chr6:132291785-132351866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9388953	VNN1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132275600-132299800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:132276600-132297800	Weak transcription	Ovary	ovary
3	chr6:132277400-132305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:132285400-132297800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:132290000-132298000	Weak transcription	Fetal Lung	lung
6	chr6:132292800-132301600	Weak transcription	Stomach Mucosa	stomach
7	chr6:132294800-132297600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:132296600-132299200	Enhancers	Osteobl	bone
9	chr6:132296600-132304400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:132296800-132301400	Weak transcription	Fetal Kidney	kidney
11	chr6:132297000-132305400	Enhancers	Liver	Liver
12	chr6:132297200-132299000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:132297200-132299000	Enhancers	Fetal Heart	heart
14	chr6:132297400-132298400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:132297400-132298400	Flanking Active TSS	HepG2	liver
16	chr6:132297400-132298600	Enhancers	NH-A	brain
17	chr6:132297400-132298800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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