Variant report

Variant	rs6663243
Chromosome Location	chr1:58709895-58709896
allele	A/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:13)

rs_ID	r²[population]
rs1974288	0.82[EUR][1000 genomes]
rs480949	0.95[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4912184	0.95[CEU][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4912313	0.83[EUR][1000 genomes]
rs494214	0.85[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs495179	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs553133	0.95[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs562867	0.95[CEU][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs577005	0.95[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs626282	0.82[EUR][1000 genomes]
rs644734	0.83[EUR][1000 genomes]
rs6662819	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs946308	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv546307	chr1:58707111-58733050	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6663243	INADL	cis	parietal	SCAN
rs6663243	DAB1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58702200-58713000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:58705200-58713000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:58705400-58712400	Weak transcription	Fetal Brain Male	brain
4	chr1:58709600-58710000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:58709800-58710000	Enhancers	Brain Cingulate Gyrus	brain

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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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