Variant report

Variant	rs1506545
Chromosome Location	chr4:125805537-125805538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10012927	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10034686	0.87[ASN][1000 genomes]
rs11732371	0.86[ASN][1000 genomes]
rs12506187	0.86[ASN][1000 genomes]
rs1351748	0.89[ASN][1000 genomes]
rs1354741	0.82[EUR][1000 genomes]
rs1395326	0.85[EUR][1000 genomes]
rs1506547	0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs17008772	0.84[YRI][hapmap]
rs2390739	0.82[EUR][1000 genomes]
rs2390740	0.86[CHD][hapmap];0.82[EUR][1000 genomes]
rs35904122	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6834395	0.82[EUR][1000 genomes]
rs6856783	0.82[EUR][1000 genomes]
rs7679784	0.89[ASN][1000 genomes]
rs9993381	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9996242	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011752	chr4:125708756-125932456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1001338	chr4:125708756-126103293	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv830050	chr4:125717858-125888563	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv879884	chr4:125791252-125841892	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv879885	chr4:125791252-125852874	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv879886	chr4:125791252-125856465	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1506545	TRPC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125798200-125820800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:125804400-125806000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:125804600-125806000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr4:125804800-125805600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:125804800-125805600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:125804800-125806000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:125805200-125806000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:125805400-125805800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:125805400-125806000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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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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