Variant report

Variant	rs2421805
Chromosome Location	chr1:71339748-71339749
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10443262	1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1536261	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4649932	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs66515565	0.98[ASN][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	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830148	chr1:71310366-71483932	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2421805	SGIP1	cis	cerebellum	SCAN
rs2421805	CASP1	trans	lymphoblastoid	seeQTL
rs2421805	DDX3Y	trans	lymphoblastoid	seeQTL
rs2421805	TCTEX1D1	cis	parietal	SCAN
rs2421805	KDM5D	trans	lymphoblastoid	seeQTL
rs2421805	RPS4Y1	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71330800-71343200	Weak transcription	K562	blood
2	chr1:71338800-71339800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:71338800-71339800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:71338800-71339800	Weak transcription	Fetal Heart	heart
5	chr1:71338800-71339800	Weak transcription	Right Atrium	heart
6	chr1:71338800-71340400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:71339000-71339800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:71339000-71339800	Enhancers	Adipose Nuclei	Adipose
9	chr1:71339000-71339800	Enhancers	NHEK	skin
10	chr1:71339000-71340400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:71339000-71341000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:71339400-71340000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:71339400-71340200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:71339400-71340800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:71339600-71340800	Enhancers	Monocytes-CD14+_RO01746	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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