Variant report

Variant	rs2886199
Chromosome Location	chr1:215885838-215885839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:215878674..215880507-chr1:215885642..215887542,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11120605	0.84[ASW][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs11120606	0.84[ASW][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12122359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140451	0.84[ASW][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs12403674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs12404185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408717	0.84[ASW][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs1342765	0.84[ASW][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2364859	0.83[CEU][hapmap];0.94[EUR][1000 genomes]
rs2364862	0.87[CHB][hapmap]
rs2820691	0.81[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2820703	0.81[ASN][1000 genomes]
rs2886198	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3845525	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845527	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372227	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4375233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4628479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4655285	0.80[YRI][hapmap]
rs4655286	0.87[CHB][hapmap]
rs4655419	0.83[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs4655423	0.93[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap]
rs4655426	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs57472918	0.94[EUR][1000 genomes]
rs61828172	0.94[EUR][1000 genomes]
rs6665313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][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	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv873171	chr1:215825167-215925167	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2886199	C1orf97	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links