Variant report

Variant	rs3913375
Chromosome Location	chr16:10090695-10090696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:10089198..10091146-chr16:10092228..10094129,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10500370	0.81[CEU][hapmap];0.86[CHD][hapmap];0.84[AMR][1000 genomes]
rs10500371	0.81[CEU][hapmap]
rs10500373	0.83[CHD][hapmap]
rs11642357	0.81[CHD][hapmap]
rs1213316	0.81[CEU][hapmap]
rs1213319	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs17682922	0.88[CHD][hapmap]
rs17750208	0.81[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17750303	0.81[CEU][hapmap];0.86[CHD][hapmap];0.84[AMR][1000 genomes]
rs2650424	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2650431	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2650434	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2729593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36061863	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3859123	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3859125	0.81[CEU][hapmap];0.81[CHD][hapmap];0.81[AMR][1000 genomes]
rs3859126	0.81[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs4363863	0.88[CHD][hapmap]
rs9788936	0.86[AMR][1000 genomes]
rs9788939	0.84[AMR][1000 genomes]
rs9921906	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949196	chr16:9937980-10182349	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1037001	chr16:10008023-10476482	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422500	chr16:10008309-10415517	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1045882	chr16:10025402-10117992	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1052566	chr16:10033178-10260068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2758410	chr16:10060976-10257550	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2758629	chr16:10060976-10257550	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv427973	chr16:10060976-10257550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1037707	chr16:10078790-10529893	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3913375	GRIN2A	cis	cerebellum	SCAN
rs3913375	DEXI	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:10090000-10090800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr16:10090600-10095800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links