Variant report

Variant	rs9405214
Chromosome Location	chr6:3963841-3963842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13205752	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap]
rs4377826	0.83[ASN][1000 genomes]
rs4959911	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs583782	1.00[YRI][hapmap]
rs6921120	0.85[JPT][hapmap]
rs7743464	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs9328208	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378391	0.82[ASN][1000 genomes]
rs9378831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9378834	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405686	0.81[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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9405214	FOXF2	cis	parietal	SCAN
rs9405214	C6orf201	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3960800-3964000	Enhancers	NH-A	brain
2	chr6:3961600-3965600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:3962000-3965200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:3962800-3964000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:3962800-3964000	Enhancers	HUVEC	blood vessel
6	chr6:3963000-3964800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:3963200-3964000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:3963200-3964200	Enhancers	Fetal Heart	heart
9	chr6:3963200-3964800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:3963400-3964400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:3963400-3964600	Enhancers	Fetal Muscle Leg	muscle
12	chr6:3963400-3965000	Weak transcription	NHDF-Ad	bronchial
13	chr6:3963400-3965400	Weak transcription	Osteobl	bone
14	chr6:3963600-3964000	Bivalent Enhancer	HepG2	liver
15	chr6:3963800-3964000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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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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