Variant report

Variant	rs11197620
Chromosome Location	chr10:118040571-118040572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10218849	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10787638	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs10787639	0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs10885889	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs11197611	0.90[GIH][hapmap];0.82[EUR][1000 genomes]
rs11197612	0.86[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11599593	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12413585	0.80[GIH][hapmap]
rs12768041	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12774375	0.90[GIH][hapmap];0.82[EUR][1000 genomes]
rs1419874	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901100	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap]
rs2901101	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs3740572	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4554795	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs4751959	0.82[EUR][1000 genomes]
rs7078853	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7087136	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	esv3449389	chr10:117806874-118102404	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832000	chr10:117944492-118116253	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11197620	GPD1L	trans	cerebellum	SCAN
rs11197620	TRUB1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:118034400-118040800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:118034600-118043000	Weak transcription	Fetal Stomach	stomach
3	chr10:118038600-118041200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:118039000-118042800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:118039600-118041000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr10:118040400-118041600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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

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