Variant report

Variant	rs1442531
Chromosome Location	chr9:17440987-17440988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1318162	0.81[EUR][1000 genomes]
rs1442530	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808894	0.81[EUR][1000 genomes]
rs2584536	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2584537	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2593382	0.90[EUR][1000 genomes]
rs2780198	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv892668	chr9:17371690-17532840	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892670	chr9:17378776-17507277	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv523411	chr9:17394536-17454799	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1442531	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
3	chr9:17412200-17443600	Weak transcription	Ovary	ovary
4	chr9:17425400-17449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:17426400-17466800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:17431000-17453400	Weak transcription	Fetal Lung	lung
7	chr9:17434000-17453600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:17434000-17453600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:17436000-17447200	Weak transcription	Lung	lung
10	chr9:17436000-17448600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:17436000-17448800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:17439400-17466800	Weak transcription	NHDF-Ad	bronchial
13	chr9:17440000-17441200	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr9:17440200-17441200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr9:17440400-17494600	Weak transcription	Left Ventricle	heart
16	chr9:17440600-17447000	Weak transcription	Fetal Stomach	stomach
17	chr9:17440800-17441000	ZNF genes & repeats	Liver	Liver
18	chr9:17440800-17441400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr9:17440800-17442200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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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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