Variant report

Variant	rs9409658
Chromosome Location	chr9:94548490-94548491
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4378021	0.80[TSI][hapmap]
rs4497030	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv523940	chr9:94546564-94573753	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9409658	ASPN	cis	parietal	SCAN
rs9409658	S1PR3	cis	parietal	SCAN
rs9409658	NXNL2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94533400-94549600	Weak transcription	Colonic Mucosa	Colon
2	chr9:94538000-94548800	Weak transcription	Esophagus	oesophagus
3	chr9:94543400-94549200	Enhancers	Colon Smooth Muscle	Colon
4	chr9:94543600-94551200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:94543800-94549000	Weak transcription	Fetal Heart	heart
6	chr9:94544600-94551000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:94545400-94553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:94545400-94555800	Weak transcription	Ovary	ovary
9	chr9:94546000-94549800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:94546800-94549200	Enhancers	Stomach Smooth Muscle	stomach
11	chr9:94547800-94549000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:94547800-94552800	Weak transcription	NHDF-Ad	bronchial
13	chr9:94548000-94552400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:94548200-94549600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:94548200-94557800	Weak transcription	Fetal Lung	lung
16	chr9:94548400-94548800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:94548400-94548800	Enhancers	K562	blood
18	chr9:94548400-94549400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:94548400-94549400	Enhancers	Rectal Smooth Muscle	rectum

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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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