Variant report

Variant	rs9948409
Chromosome Location	chr18:24761928-24761929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1155610	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11662578	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11872883	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12965259	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1426876	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1426877	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1426879	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4800787	0.85[EUR][1000 genomes]
rs4800797	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508476	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6508478	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8088724	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9332435	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9947201	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9947302	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9947640	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9947927	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9951209	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956654	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9959121	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909473	chr18:24655235-24792075	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv909474	chr18:24683823-24832023	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv909475	chr18:24687324-24776226	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv530515	chr18:24704459-24883897	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv909476	chr18:24722839-24779601	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1810563	chr18:24727747-24773141	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9948409	CHST9	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24756200-24762200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr18:24756200-24764000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr18:24756600-24764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:24757800-24764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:24758200-24762600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr18:24758200-24762800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr18:24758200-24762800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr18:24758200-24762800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr18:24758200-24762800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:24758200-24763000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr18:24758800-24763200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:24760400-24762600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr18:24761200-24763400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr18:24761600-24763200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr18:24761600-24764000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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