Variant report

Variant	rs2220521
Chromosome Location	chr3:159150435-159150436
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13434321	0.86[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs1375409	0.82[CEU][hapmap]
rs1448999	0.86[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs1449004	0.86[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.85[TSI][hapmap]
rs1449013	0.82[CEU][hapmap]
rs1489922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1515627	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs2621302	0.86[CEU][hapmap]
rs4086062	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679856	0.82[CEU][hapmap]
rs6782775	0.86[CEU][hapmap]
rs7621541	0.82[CEU][hapmap]
rs7643870	0.86[CEU][hapmap]
rs9290040	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]

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	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1004990	chr3:159090974-159174954	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2220521	SCHIP1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159149600-159151800	Enhancers	Fetal Brain Male	brain
2	chr3:159149800-159151600	Enhancers	Fetal Brain Female	brain
3	chr3:159149800-159151800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:159149800-159152400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:159150200-159151000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:159150200-159151400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:159150400-159150800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:159150400-159151200	Enhancers	Brain Germinal Matrix	brain

Quick Search:

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

what's new

Quick links