Variant report

Variant	rs4539203
Chromosome Location	chr1:217238322-217238323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11117765	0.81[AMR][1000 genomes]
rs1166344	0.81[MKK][hapmap]
rs12031786	0.81[AMR][1000 genomes]
rs1339225	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs17045141	0.85[CHD][hapmap]
rs2225968	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4537652	0.85[CHD][hapmap]
rs4846808	0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs4846809	0.89[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs4846810	0.81[AMR][1000 genomes]
rs4846812	1.00[ASW][hapmap]
rs924652	0.80[CEU][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs950482	0.82[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][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	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4539203	C1orf227	cis	parietal	SCAN
rs4539203	USH2A	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217213400-217240600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:217221800-217251400	Weak transcription	Left Ventricle	heart
3	chr1:217223200-217250000	Weak transcription	Psoas Muscle	Psoas
4	chr1:217236000-217249400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:217237000-217249400	Weak transcription	Pancreas	Pancrea
6	chr1:217237200-217238400	Weak transcription	Fetal Heart	heart
7	chr1:217237200-217238800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:217237200-217246200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:217238000-217239200	Weak transcription	Fetal Intestine Large	intestine

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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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