Variant report

Variant	rs214680
Chromosome Location	chr12:47679348-47679349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs214673	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs214676	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs214677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs214678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs214679	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs214682	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs855184	0.82[CEU][hapmap];0.82[JPT][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs855185	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[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	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv527663	chr12:47676950-47679348	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs214680	FAM113B	cis	parietal	SCAN
rs214680	TMEM106C	cis	parietal	SCAN
rs214680	FKBP11	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47672800-47680200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:47676200-47697200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:47676800-47680400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:47676800-47680400	Weak transcription	HSMMtube	muscle
5	chr12:47676800-47687600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:47677800-47680200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:47679200-47679400	Enhancers	A549	lung

Quick Search:

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

what's new

Quick links