Variant report

Variant	rs1028838
Chromosome Location	chr10:4401172-4401173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10904240	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11814820	1.00[CHB][hapmap]
rs1547179	0.85[CHB][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs1571130	0.81[AFR][1000 genomes]
rs1679448	0.85[GIH][hapmap];0.88[MEX][hapmap]
rs1679449	0.85[GIH][hapmap];0.83[MEX][hapmap]
rs1751312	0.85[GIH][hapmap];0.88[MEX][hapmap]
rs1926803	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1926810	0.81[AFR][1000 genomes]
rs1926813	0.81[AFR][1000 genomes]
rs1926814	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148606	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601839	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7082366	0.81[AFR][1000 genomes]
rs7894528	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7906485	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7914563	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs966935	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[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	nsv894786	chr10:4385379-4441989	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1028838	GDI2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4395400-4401200	Weak transcription	Adipose Nuclei	Adipose
2	chr10:4397400-4402400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:4400200-4402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:4400800-4401800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:4401000-4401400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:4401000-4401400	Enhancers	Fetal Lung	lung
7	chr10:4401000-4401600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr10:4401000-4401600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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