Variant report

Variant	rs9380696
Chromosome Location	chr6:37600774-37600775
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10485031	1.00[CHB][hapmap]
rs10755699	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1619327	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738454	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639655	1.00[CHB][hapmap]
rs1776447	1.00[CHB][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs3846877	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs3887743	1.00[CHB][hapmap]
rs4236057	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6911875	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6915583	1.00[CHB][hapmap]
rs6922589	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs804828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804840	1.00[CHB][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs804841	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9380696	FGD2	cis	parietal	SCAN
rs9380696	KIF6	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37594000-37615400	Weak transcription	Fetal Brain Female	brain
2	chr6:37594200-37602200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:37598800-37606400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:37598800-37606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:37599000-37605800	Weak transcription	A549	lung
6	chr6:37599200-37602200	Weak transcription	Esophagus	oesophagus
7	chr6:37599200-37615600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:37599200-37621800	Weak transcription	NHLF	lung
9	chr6:37599400-37601800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:37599800-37600800	Weak transcription	Spleen	Spleen
11	chr6:37599800-37603600	Weak transcription	Hela-S3	cervix
12	chr6:37600400-37600800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr6:37600400-37611400	Weak transcription	Primary B cells from peripheral blood	blood

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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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