Variant report

Variant	rs2409701
Chromosome Location	chr8:10957723-10957724
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10108618	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1057626	0.88[EUR][1000 genomes]
rs2409698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34069332	0.85[EUR][1000 genomes]
rs4523214	0.82[EUR][1000 genomes]
rs4840544	0.89[EUR][1000 genomes]
rs4841495	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6601559	0.83[EUR][1000 genomes]
rs6601560	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6601561	0.85[EUR][1000 genomes]
rs6601562	0.89[EUR][1000 genomes]
rs6991930	0.87[EUR][1000 genomes]
rs7820860	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7835318	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7844895	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2409701	AF131215.2	cis	Nerve Tibial	GTEx
rs2409701	AF131215.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2409701	AF131215.9	cis	Nerve Tibial	GTEx
rs2409701	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2409701	AF131215.2	cis	Stomach	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10950600-10965000	Weak transcription	Gastric	stomach
2	chr8:10954400-10959200	Weak transcription	Pancreas	Pancrea
3	chr8:10955200-10968000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:10956800-10964800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:10957200-10964800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr8:10957600-10958600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr8:10957600-10958600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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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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