Variant report

Variant	rs6884405
Chromosome Location	chr5:118352079-118352080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1473231	1.00[JPT][hapmap]
rs1473337	1.00[JPT][hapmap]
rs1510969	1.00[JPT][hapmap]
rs17144738	1.00[JPT][hapmap]
rs17144795	1.00[JPT][hapmap]
rs17144818	1.00[JPT][hapmap]
rs17144857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17144865	1.00[ASN][1000 genomes]
rs17144871	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2055620	1.00[JPT][hapmap]
rs2161349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs2197797	1.00[JPT][hapmap]
rs4421136	1.00[JPT][hapmap]
rs6869894	1.00[JPT][hapmap]
rs71577045	0.87[ASN][1000 genomes]
rs7708024	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7719887	1.00[JPT][hapmap]
rs7722027	1.00[JPT][hapmap]
rs976586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[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	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6884405	DMXL1	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118349400-118353400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:118350400-118355200	Enhancers	Primary B cells from cord blood	blood
3	chr5:118350600-118360000	Enhancers	Primary B cells from peripheral blood	blood
4	chr5:118351600-118352200	ZNF genes & repeats	GM12878-XiMat	blood
5	chr5:118351600-118354400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr5:118351600-118359800	Enhancers	Primary monocytes fromperipheralblood	blood

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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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