Variant report

Variant	rs12410279
Chromosome Location	chr1:220851520-220851521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220848519..220851962-chr1:220854951..220857000,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1073460	0.86[CHB][hapmap]
rs12032280	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407624	0.80[CEU][hapmap]
rs12563921	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564479	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1472253	0.87[AMR][1000 genomes]
rs1933002	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs1933008	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs2253641	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs2378401	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2378402	0.80[ASN][1000 genomes]
rs2589588	0.86[CHB][hapmap]
rs2786601	0.86[CHB][hapmap]
rs2786604	0.86[CHB][hapmap]
rs2786613	0.86[CHB][hapmap]
rs2786619	0.82[CHB][hapmap]
rs337182	0.90[CEU][hapmap]
rs3806329	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4846657	0.85[CHD][hapmap]
rs4846658	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61830219	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541155	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6677302	0.84[ASN][1000 genomes]
rs6689349	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6699189	0.87[CHB][hapmap]
rs6699196	0.86[CHB][hapmap]
rs72629673	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7514431	0.80[ASN][1000 genomes]
rs774139	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS 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
4	nsv945302	chr1:220851349-220854713	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12410279	C1orf115	cis	cerebellum	SCAN
rs12410279	MOSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220848000-220853600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:220851200-220852000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links