Variant report

Variant	rs491699
Chromosome Location	chr1:93499628-93499629
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10874754	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164862	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs11164865	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590314	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12084977	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091867	0.99[EUR][1000 genomes]
rs12092136	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12094815	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2485031	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2785601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs569268	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59284207	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61523335	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6657919	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6686863	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688632	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103530	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536849	0.87[AMR][1000 genomes];0.93[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs491699	KIAA1107	cis	cerebellum	SCAN
rs491699	TMED5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93488000-93504200	Enhancers	Fetal Thymus	thymus
2	chr1:93495800-93504200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:93496800-93503600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:93498400-93500200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:93498400-93500200	Enhancers	Thymus	Thymus
6	chr1:93498400-93500400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:93498600-93500200	Enhancers	Primary B cells from cord blood	blood
8	chr1:93499400-93499800	Enhancers	K562	blood
9	chr1:93499400-93500400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:93499400-93505000	Enhancers	Dnd41	blood
11	chr1:93499600-93499800	Enhancers	GM12878-XiMat	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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