Variant report

Variant	rs10908647
Chromosome Location	chr1:158293942-158293943
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10797008	0.97[ASN][1000 genomes]
rs10908646	1.00[ASN][1000 genomes]
rs10908648	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12037117	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12038925	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12084190	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2317883	1.00[ASN][1000 genomes]
rs3176842	1.00[ASN][1000 genomes]
rs3176843	1.00[ASN][1000 genomes]
rs3181029	1.00[CEU][hapmap]
rs34591069	0.92[ASN][1000 genomes]
rs35752748	0.92[ASN][1000 genomes]
rs4489554	0.96[ASN][1000 genomes]
rs55852659	0.80[EUR][1000 genomes]
rs59038586	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60706492	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs716221	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs73029766	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv831692	chr1:158223459-158392016	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10908647	OR6K6	cis	parietal	SCAN
rs10908647	RAG1AP1	cis	cerebellum	SCAN
rs10908647	KRTCAP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158292600-158294200	ZNF genes & repeats	Fetal Thymus	thymus
2	chr1:158292600-158294200	ZNF genes & repeats	Dnd41	blood
3	chr1:158293400-158294000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
4	chr1:158293400-158294200	ZNF genes & repeats	Thymus	Thymus
5	chr1:158293600-158294000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr1:158293800-158294800	Enhancers	GM12878-XiMat	blood
7	chr1:158293800-158298200	Weak transcription	Primary B cells from cord blood	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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