Variant report

Variant	rs10803666
Chromosome Location	chr2:234838947-234838948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1004478	0.93[CEU][hapmap]
rs10490010	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803665	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11562954	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470426	0.85[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs12473889	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13028228	1.00[CEU][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17862920	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs17862921	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs17863838	0.93[CEU][hapmap]
rs17863841	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17863842	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17864741	0.93[CEU][hapmap]
rs17868384	0.92[EUR][1000 genomes]
rs6741751	0.93[CEU][hapmap]
rs67646620	0.92[EUR][1000 genomes]
rs7558436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7562952	1.00[CEU][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs7562971	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7577262	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs9646718	0.93[CEU][hapmap]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10803666	COL6A3	cis	cerebellum	SCAN
rs10803666	APOBEC3B	trans	cerebellum	SCAN
rs10803666	NMUR1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234837400-234839000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr2:234837600-234839000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:234837600-234839000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr2:234837800-234839000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr2:234838400-234839400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:234838400-234839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:234838400-234841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:234838600-234841000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:234838800-234839200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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