Variant report

Variant	rs6539213
Chromosome Location	chr12:105848874-105848875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10861430	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526854	0.87[ASN][1000 genomes]
rs6539212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv899501	chr12:105819046-105950801	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv832507	chr12:105821685-106005186	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1045689	chr12:105836970-105879110	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6539213	MTERFD3	cis	parietal	SCAN
rs6539213	PAH	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105841600-105850400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:105845800-105850600	Weak transcription	HSMM	muscle
3	chr12:105845800-105850800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:105845800-105850800	Weak transcription	HSMMtube	muscle
5	chr12:105846000-105850600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:105847000-105850800	Weak transcription	Aorta	Aorta
7	chr12:105847600-105851000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:105848400-105849200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:105848400-105849400	Enhancers	HUVEC	blood vessel
10	chr12:105848400-105849800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:105848600-105849200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:105848600-105849400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:105848600-105849800	Enhancers	NHEK	skin
14	chr12:105848800-105849000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr12:105848800-105849200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:105848800-105849200	Enhancers	Right Atrium	heart
17	chr12:105848800-105849400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:105848800-105849400	Enhancers	Psoas Muscle	Psoas
19	chr12:105848800-105854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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