Variant report

Variant	rs703623
Chromosome Location	chr12:104034955-104034956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1018033	0.84[MEX][hapmap]
rs1427798	0.84[CHB][hapmap]
rs1650123	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1650124	0.99[ASN][1000 genomes]
rs2673654	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs703614	0.85[CHB][hapmap];0.87[MEX][hapmap]
rs703616	0.85[CHB][hapmap];0.91[MEX][hapmap]
rs703618	0.84[CHB][hapmap];0.91[MEX][hapmap]
rs703619	0.85[CHB][hapmap];0.91[MEX][hapmap]
rs703624	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs703625	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs703627	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs703632	0.95[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703633	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958947	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs831427	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[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	nsv1052275	chr12:104008918-104044241	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv527362	chr12:104029462-104038974	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv865	chr12:104030102-104074864	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs703623	NT5DC3	cis	cerebellum	SCAN
rs703623	IGF1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104027000-104037200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:104033200-104062200	Weak transcription	Spleen	Spleen
3	chr12:104034200-104035200	Flanking Active TSS	GM12878-XiMat	blood
4	chr12:104034200-104040600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:104034400-104035400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:104034400-104035400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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