Variant report

Variant	rs2409742
Chromosome Location	chr8:11069960-11069961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11058254..11060628-chr8:11068352..11070354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171044	Chromatin interaction
ENSG00000270076	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10087081	1.00[CHB][hapmap]
rs10093053	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10106207	0.82[CHB][hapmap]
rs10106914	1.00[CHB][hapmap]
rs10108347	0.80[EUR][1000 genomes]
rs10109167	0.80[EUR][1000 genomes]
rs10503416	1.00[CHB][hapmap]
rs11250119	1.00[CHB][hapmap]
rs11250121	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724467	1.00[CHB][hapmap]
rs17783634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001329	0.82[CHB][hapmap]
rs2409710	1.00[CHB][hapmap]
rs2409712	1.00[CHB][hapmap]
rs2409713	0.82[CHB][hapmap]
rs2409714	0.82[CHB][hapmap]
rs2409715	0.82[CHB][hapmap]
rs2409716	0.82[CHB][hapmap]
rs2409718	0.82[CHB][hapmap]
rs2409722	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409724	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2736313	0.81[AMR][1000 genomes]
rs28633434	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3021494	1.00[CHB][hapmap]
rs4333549	1.00[CHB][hapmap]
rs4523214	1.00[CHB][hapmap]
rs4557666	0.81[ASN][1000 genomes]
rs4840549	0.82[CHB][hapmap]
rs4841498	1.00[CHB][hapmap]
rs4841500	1.00[CHB][hapmap]
rs4841501	0.82[CHB][hapmap]
rs4841507	0.82[CHB][hapmap]
rs6601564	1.00[CHB][hapmap]
rs6601565	0.82[AMR][1000 genomes]
rs6601570	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6981523	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986032	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes]
rs6996752	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7010590	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7813802	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7819412	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7823349	0.82[CHB][hapmap]
rs7829396	0.82[CHB][hapmap]
rs9329240	0.92[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	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	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2409742	AF131215.2	cis	Nerve Tibial	GTEx
rs2409742	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2409742	AF131215.2	cis	Stomach	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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