Variant report

Variant	rs6842830
Chromosome Location	chr4:55873926-55873927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10008166	0.82[ASN][1000 genomes]
rs12649965	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs28804476	0.86[ASN][1000 genomes]
rs28888809	0.86[ASN][1000 genomes]
rs4269235	0.88[ASN][1000 genomes]
rs4274913	0.83[ASN][1000 genomes]
rs4328969	0.88[ASN][1000 genomes]
rs4346706	0.86[ASN][1000 genomes]
rs4463123	0.89[ASN][1000 genomes]
rs4495108	0.86[ASN][1000 genomes]
rs4634284	0.85[ASN][1000 genomes]
rs56201409	0.85[ASN][1000 genomes]
rs56316114	0.86[ASN][1000 genomes]
rs56384539	0.88[ASN][1000 genomes]
rs6821465	0.87[ASN][1000 genomes]
rs6832059	0.85[ASN][1000 genomes]
rs6835585	0.84[ASN][1000 genomes]
rs7696684	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv948758	chr4:55748430-55887962	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829939	chr4:55856771-56005011	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS 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	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6842830	TXNDC9	cis	cerebellum	SCAN
rs6842830	SCFD2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55870800-55877400	Weak transcription	Fetal Lung	lung
2	chr4:55871200-55875200	Weak transcription	Right Atrium	heart
3	chr4:55871400-55875200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:55872000-55874000	Weak transcription	Adipose Nuclei	Adipose
5	chr4:55872800-55874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:55872800-55883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:55873000-55883000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:55873600-55875400	Enhancers	HUVEC	blood vessel
9	chr4:55873800-55874800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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