Variant report

Variant	rs16854229
Chromosome Location	chr1:179496680-179496681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10494515	0.81[JPT][hapmap]
rs10494516	0.81[JPT][hapmap]
rs10494520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753191	0.85[JPT][hapmap]
rs10798665	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs10798670	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs10913733	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10913734	0.85[JPT][hapmap]
rs10913758	0.83[AMR][1000 genomes]
rs10913806	0.88[CHB][hapmap]
rs10913816	0.81[JPT][hapmap]
rs12073906	0.83[AMR][1000 genomes]
rs12073970	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12097041	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs12118625	0.88[AMR][1000 genomes]
rs12120123	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12130876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12131473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12131475	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs12132906	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12134114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12135209	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12138436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12138619	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12140299	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405133	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12405321	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12406695	0.82[ASN][1000 genomes]
rs12408477	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs12736300	0.87[ASN][1000 genomes]
rs12740270	0.87[ASN][1000 genomes]
rs12740455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs12745772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12759446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1329276	0.88[CHB][hapmap];0.82[CHD][hapmap]
rs13306731	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs13374852	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16854009	0.94[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs1887816	0.81[JPT][hapmap]
rs2274623	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2274625	0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28508518	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34816244	0.86[ASN][1000 genomes]
rs35954891	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36068644	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753526	0.85[JPT][hapmap]
rs3767841	0.81[JPT][hapmap]
rs3829795	0.81[JPT][hapmap]
rs4077551	1.00[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs4077552	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4133136	1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs61826054	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61826055	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827681	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669967	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs71514854	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9660720	0.83[AMR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16854229	ABL2	cis	cerebellum	SCAN
rs16854229	TNR	cis	cerebellum	SCAN
rs16854229	ABL2	cis	parietal	SCAN
rs16854229	FAM20B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179486400-179499600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179486600-179499600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:179493800-179498000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:179494200-179497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:179494200-179497200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:179494200-179497200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:179494200-179497400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:179494200-179498400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:179496200-179498200	Enhancers	HUES48 Cell Line	embryonic stem cell

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