Variant report

Variant	rs9844730
Chromosome Location	chr3:144216886-144216887
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1036439	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10490827	0.87[ASN][1000 genomes]
rs10935507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631899	0.87[ASN][1000 genomes]
rs12632855	0.86[ASN][1000 genomes]
rs12638468	0.91[ASN][1000 genomes]
rs12638544	0.91[ASN][1000 genomes]
rs12639461	0.88[ASN][1000 genomes]
rs13066453	0.81[ASN][1000 genomes]
rs13081974	0.90[ASN][1000 genomes]
rs1527238	0.81[ASN][1000 genomes]
rs1657010	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2575189	0.83[EUR][1000 genomes]
rs2694959	0.81[EUR][1000 genomes]
rs2717388	0.83[EUR][1000 genomes]
rs2717389	0.83[EUR][1000 genomes]
rs34130084	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4290842	0.92[ASN][1000 genomes]
rs4388021	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4479640	0.81[ASN][1000 genomes]
rs4681125	0.81[ASN][1000 genomes]
rs4681126	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4681342	0.81[ASN][1000 genomes]
rs56096828	0.87[ASN][1000 genomes]
rs56178175	0.92[ASN][1000 genomes]
rs56191622	0.81[ASN][1000 genomes]
rs56228220	0.87[ASN][1000 genomes]
rs57393618	0.88[ASN][1000 genomes]
rs59900584	0.86[ASN][1000 genomes]
rs61641065	0.81[ASN][1000 genomes]
rs6440258	0.80[ASN][1000 genomes]
rs6799623	0.80[ASN][1000 genomes]
rs721029	0.83[EUR][1000 genomes]
rs721030	0.83[EUR][1000 genomes]
rs73009099	0.92[ASN][1000 genomes]
rs73871205	0.92[ASN][1000 genomes]
rs73871207	0.92[ASN][1000 genomes]
rs73871211	0.88[ASN][1000 genomes]
rs73871221	0.86[ASN][1000 genomes]
rs73875119	0.92[ASN][1000 genomes]
rs73875127	0.92[ASN][1000 genomes]
rs73875134	0.92[ASN][1000 genomes]
rs73875140	0.92[ASN][1000 genomes]
rs7613977	0.83[ASN][1000 genomes]
rs7615146	0.80[ASN][1000 genomes]
rs7616429	0.81[ASN][1000 genomes]
rs7620611	0.83[ASN][1000 genomes]
rs7630402	0.87[ASN][1000 genomes]
rs7634647	0.81[ASN][1000 genomes]
rs7636316	0.86[ASN][1000 genomes]
rs7637942	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653820	0.80[ASN][1000 genomes]
rs920146	0.89[ASN][1000 genomes]
rs9833354	0.80[ASN][1000 genomes]
rs9840395	0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9866198	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866442	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873732	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878902	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.81[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	nsv532633	chr3:143802417-144440646	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1011685	chr3:143959237-144218424	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536751	chr3:143959237-144218424	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2756108	chr3:144177836-144301659	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877571	chr3:144188561-144291254	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9844730	COMMD2	cis	parietal	SCAN
rs9844730	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144215400-144217400	Weak transcription	HUVEC	blood vessel
2	chr3:144215600-144220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:144216400-144221000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:144216600-144221000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links