Variant report

Variant	rs1838344
Chromosome Location	chr12:10956749-10956750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10743925	0.86[AFR][1000 genomes]
rs10743926	0.86[AFR][1000 genomes]
rs10772362	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1548803	0.90[AFR][1000 genomes]
rs1838345	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1838346	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2588350	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741845	0.94[ASN][1000 genomes]
rs615239	0.89[ASN][1000 genomes]
rs655046	0.94[ASN][1000 genomes]
rs689118	0.83[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	nsv1049362	chr12:10893573-11018850	Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv898776	chr12:10909412-11032045	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1838344	PRR4	cis	Thyroid	GTEx
rs1838344	RP11-785H5.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10955600-10960600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:10955600-10961000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:10955800-10958000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:10955800-10960400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:10955800-10961000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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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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