Variant report

Variant	rs6479458
Chromosome Location	chr9:95930334-95930335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10119816	0.95[ASN][1000 genomes]
rs10761208	0.85[GIH][hapmap]
rs1111776	0.85[GIH][hapmap]
rs12684392	0.85[GIH][hapmap]
rs56311541	0.95[ASN][1000 genomes]
rs58965550	0.85[ASN][1000 genomes]
rs7021769	0.96[EUR][1000 genomes]
rs7022051	1.00[JPT][hapmap]
rs7024425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7025060	0.95[EUR][1000 genomes]
rs7035727	0.95[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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6479458	NINJ1	cis	cerebellum	SCAN
rs6479458	SECISBP2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95907200-95944400	Weak transcription	Right Atrium	heart
2	chr9:95922400-95930600	Weak transcription	Right Ventricle	heart
3	chr9:95923000-95930600	Weak transcription	Pancreas	Pancrea
4	chr9:95924600-95930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:95925000-95933800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:95925400-95930600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:95929000-95930800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:95929000-95931000	Enhancers	Placenta	Placenta
9	chr9:95929200-95930400	Enhancers	Duodenum Mucosa	Duodenum
10	chr9:95929400-95930600	Weak transcription	Stomach Mucosa	stomach
11	chr9:95929400-95930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:95929400-95931000	Enhancers	Fetal Muscle Trunk	muscle
13	chr9:95929400-95931200	Enhancers	Fetal Muscle Leg	muscle
14	chr9:95929400-95931600	Enhancers	HepG2	liver
15	chr9:95929600-95931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:95930000-95930400	Enhancers	Fetal Stomach	stomach
17	chr9:95930200-95930400	Enhancers	Fetal Lung	lung
18	chr9:95930200-95931600	Enhancers	Left Ventricle	heart

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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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