Variant report

Variant	rs9468841
Chromosome Location	chr6:30825287-30825288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12525616	0.84[ASN][1000 genomes]
rs3916232	0.82[AMR][1000 genomes]
rs9295928	0.86[AMR][1000 genomes]
rs9295930	0.86[AMR][1000 genomes]
rs9461639	0.81[AMR][1000 genomes]
rs9468843	0.81[AMR][1000 genomes]
rs9468850	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9501340	0.81[AMR][1000 genomes]
rs9501491	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884108	chr6:30821187-30838497	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468841	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30823200-30826400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:30823400-30825400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:30823600-30826400	Enhancers	Fetal Thymus	thymus
4	chr6:30823600-30835400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30824200-30825400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:30824400-30826000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30824400-30826200	Enhancers	Fetal Lung	lung
8	chr6:30824600-30826000	Enhancers	Fetal Stomach	stomach
9	chr6:30824800-30825400	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr6:30824800-30825600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:30825000-30825400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:30825000-30825600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:30825000-30825800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:30825000-30826200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:30825000-30826200	Bivalent Enhancer	Placenta	Placenta
16	chr6:30825200-30825400	Bivalent Enhancer	HepG2	liver
17	chr6:30825200-30825600	Flanking Active TSS	Fetal Kidney	kidney
18	chr6:30825200-30826000	Flanking Active TSS	GM12878-XiMat	blood

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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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