Variant report

Variant	rs10990447
Chromosome Location	chr9:98412987-98412988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10990491	0.87[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10991208	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10991384	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10991400	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10991546	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12551252	0.86[ASN][1000 genomes]
rs16910111	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1970200	0.85[ASN][1000 genomes]
rs915228	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1041997	chr9:98322355-98442175	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv540176	chr9:98322355-98442175	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10990447	HCP5	trans	brain	seeQTL
rs10990447	IFIT3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98411800-98413200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:98412000-98413000	Active TSS	NHDF-Ad	bronchial
3	chr9:98412600-98413000	Active TSS	Ovary	ovary
4	chr9:98412800-98413000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:98412800-98413200	Enhancers	HSMMtube	muscle
6	chr9:98412800-98413200	Active TSS	Osteobl	bone

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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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