Variant report

Variant	rs7538100
Chromosome Location	chr1:211614200-211614201
allele	C/T
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:19)

rs_ID	r²[population]
rs11577985	0.85[CHD][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap]
rs11581989	0.85[CHD][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap]
rs11582143	0.86[ASW][hapmap];0.85[CHD][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap]
rs1419090	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17017361	0.83[LWK][hapmap]
rs17017394	0.85[CHD][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap]
rs17017399	0.85[CHD][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap]
rs17017431	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17017432	0.86[ASW][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17017441	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17017451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34318448	0.81[AFR][1000 genomes]
rs61848982	0.81[AFR][1000 genomes]
rs6666324	0.89[YRI][hapmap]
rs6699139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529673	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7533617	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536058	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547352	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv945612	chr1:211593276-211615726	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7538100	LINC00467	cis	Muscle Skeletal	GTEx
rs7538100	CTSE	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211604800-211614800	Weak transcription	Gastric	stomach
2	chr1:211612200-211617400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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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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