Variant report

Variant	rs13211542
Chromosome Location	chr6:117994158-117994159
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:9)

rs_ID	r²[population]
rs10484298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11961040	0.87[ASN][1000 genomes]
rs12194183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1827327	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946273	0.82[CHD][hapmap]
rs9320617	0.82[ASN][1000 genomes]
rs9387491	0.84[CHB][hapmap]
rs9401025	0.88[ASN][1000 genomes]
rs9489238	0.80[CHD][hapmap]

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	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv5449	chr6:117954646-117999751	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13211542	FRK	cis	cerebellum	SCAN
rs13211542	MCM9	cis	parietal	SCAN
rs13211542	DCBLD1	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117969400-117995800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:117973800-117995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:117978000-117995600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:117990400-117995000	Weak transcription	HepG2	liver
5	chr6:117990600-117995200	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:117990600-117995800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:117991400-117995000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:117991600-117995400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:117991600-117996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:117991800-117995600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:117992200-117995000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:117992200-117995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:117993000-117995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:117993400-117995800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:117993600-117995200	Transcr. at gene 5' and 3'	K562	blood
16	chr6:117993600-117995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:117994000-117994200	Enhancers	GM12878-XiMat	blood

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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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