Variant report

Variant	rs7754123
Chromosome Location	chr6:132667232-132667233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1569525	0.82[CHB][hapmap]
rs17061204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2876176	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4895935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56352231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58201648	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58272798	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60561448	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6917708	0.82[CHB][hapmap]
rs73546003	1.00[EUR][1000 genomes]
rs73546006	1.00[EUR][1000 genomes]
rs73546009	1.00[EUR][1000 genomes]
rs73546020	1.00[EUR][1000 genomes]
rs73546027	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73546028	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73546029	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73546091	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771227	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886674	chr6:132613798-132694751	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv830811	chr6:132623160-132787539	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer 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 miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7754123	NCF1	trans	brain	seeQTL
rs7754123	FAM129A	trans	brain	seeQTL
rs7754123	IFI16	trans	brain	seeQTL
rs7754123	PDPN	trans	brain	seeQTL
rs7754123	S100A11	trans	brain	seeQTL
rs7754123	MTHFD2	trans	brain	seeQTL
rs7754123	SPI1	trans	brain	seeQTL
rs7754123	SLC16A3	trans	brain	seeQTL
rs7754123	LY96	trans	brain	seeQTL
rs7754123	WAS	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132644400-132675400	Weak transcription	Fetal Lung	lung
2	chr6:132656000-132676000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:132656800-132675400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:132656800-132676000	Weak transcription	NHDF-Ad	bronchial
5	chr6:132658200-132674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:132658200-132674800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:132662800-132669200	Weak transcription	Fetal Kidney	kidney
8	chr6:132666200-132674000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:132666200-132675400	Weak transcription	Osteobl	bone
10	chr6:132666400-132667600	Weak transcription	Fetal Brain Male	brain
11	chr6:132666400-132676000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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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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