Variant report

Variant	rs6439524
Chromosome Location	chr3:134537888-134537889
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1913685	0.82[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4955455	0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs4955502	0.86[TSI][hapmap]
rs4955503	0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs4955504	0.91[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6439522	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6439523	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6439524	EPHB1	cis	Artery Tibial	GTEx
rs6439524	EPHB1	cis	Esophagus Mucosa	GTEx
rs6439524	ACPP	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134529600-134541800	Weak transcription	Fetal Brain Female	brain
2	chr3:134529600-134542600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:134529600-134546400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:134530000-134540800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:134530800-134541000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:134534800-134546000	Weak transcription	Right Atrium	heart
7	chr3:134535800-134540800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:134537000-134541000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:134537000-134543000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:134537000-134543400	Weak transcription	Psoas Muscle	Psoas
11	chr3:134537800-134538000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:134537800-134539400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:134537800-134545600	Weak transcription	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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