Variant report

Variant	rs6843293
Chromosome Location	chr4:77392092-77392093
allele	A/G
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:19)

rs_ID	r²[population]
rs10002170	0.96[AFR][1000 genomes]
rs10031136	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11723732	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13146564	0.90[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13152154	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1398017	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1511817	0.82[CEU][hapmap]
rs1849215	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1949137	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2136854	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4241593	0.89[CEU][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4475168	0.96[AFR][1000 genomes]
rs4859445	0.82[CEU][hapmap]
rs4859673	0.85[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859674	0.89[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62300863	0.86[EUR][1000 genomes]
rs6532414	0.94[AFR][1000 genomes]
rs6532417	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6839100	0.80[EUR][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	esv2757941	chr4:77264596-77417457	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759262	chr4:77264596-77455405	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757069	chr4:77392092-77455405	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6843293	CCDC158	cis	parietal	SCAN
rs6843293	ART3	cis	parietal	SCAN
rs6843293	FGF5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77385600-77393000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:77386000-77393000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:77387000-77394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:77387600-77406000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:77389200-77393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:77390800-77392200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:77391000-77392200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:77391200-77392200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:77391400-77392200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:77391800-77392200	Enhancers	Brain Germinal Matrix	brain
11	chr4:77391800-77392200	Enhancers	Fetal Brain Female	brain
12	chr4:77392000-77392600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:77392000-77392800	Weak transcription	Primary T cells from cord 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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