Variant report

Variant	rs659498
Chromosome Location	chr9:116399404-116399405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1411672	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1679671	0.88[EUR][1000 genomes]
rs2039224	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2622265	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2622268	0.84[AMR][1000 genomes]
rs2622269	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2812397	0.81[AMR][1000 genomes]
rs4582632	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs589248	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590963	0.84[AMR][1000 genomes]
rs591354	0.84[AMR][1000 genomes]
rs6478026	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs657677	0.85[CEU][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116385800-116402600	Weak transcription	Stomach Mucosa	stomach
2	chr9:116389800-116402800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:116397000-116399600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:116397200-116400400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:116397200-116401200	Weak transcription	Spleen	Spleen
6	chr9:116397600-116403000	Weak transcription	Fetal Heart	heart
7	chr9:116397800-116400800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:116398800-116401200	Weak transcription	Fetal Stomach	stomach
9	chr9:116398800-116410200	Weak transcription	Right Atrium	heart
10	chr9:116399000-116401200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:116399000-116401200	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:116399000-116407400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:116399400-116401200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:116399400-116403200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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