Variant report

Variant	rs390253
Chromosome Location	chr9:107969815-107969816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12335477	0.82[JPT][hapmap]
rs13288985	0.85[MKK][hapmap]
rs167868	0.82[EUR][1000 genomes]
rs327951	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs327952	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327953	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327969	0.81[EUR][1000 genomes]
rs327970	0.89[EUR][1000 genomes]
rs327974	0.93[CEU][hapmap]
rs34151214	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029837	0.86[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1045079	chr9:107938039-107975595	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1043466	chr9:107950174-108001988	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription 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 lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs390253	SLC44A1	cis	Liver	GTEx
rs390253	SLC44A1	trans	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:107966600-107970000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:107967200-107970200	Enhancers	Fetal Lung	lung
3	chr9:107967200-107970400	Enhancers	Liver	Liver
4	chr9:107967800-107970000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:107967800-107970000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:107968000-107970000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr9:107968400-107970000	Enhancers	Adipose Nuclei	Adipose
8	chr9:107969000-107970000	Enhancers	HepG2	liver
9	chr9:107969200-107970000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:107969200-107970000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:107969400-107970000	Enhancers	Fetal Muscle Trunk	muscle
12	chr9:107969400-107970600	Enhancers	Lung	lung
13	chr9:107969600-107970000	Enhancers	NHDF-Ad	bronchial
14	chr9:107969800-107971200	Weak transcription	A549	lung

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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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