Variant report

Variant	rs1546470
Chromosome Location	chr2:48449724-48449725
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10197197	0.97[EUR][1000 genomes]
rs1112259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11678411	0.96[EUR][1000 genomes]
rs12469811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12479017	0.89[EUR][1000 genomes]
rs12713006	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713007	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13010470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1396826	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1546471	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546472	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1567397	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2175138	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2348720	0.90[EUR][1000 genomes]
rs2348723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882004	1.00[ASN][1000 genomes]
rs4375916	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4953567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62137435	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6545024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6705995	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6742830	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6755968	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs7569620	0.86[EUR][1000 genomes]
rs7578930	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7589085	0.97[EUR][1000 genomes]
rs7596628	0.90[EUR][1000 genomes]
rs876871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs906857	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1005241	chr2:48413134-48493182	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2762552	chr2:48413146-48493182	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv457407	chr2:48414735-48493182	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv581774	chr2:48414735-48493182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1001850	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv535681	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1546470	C2orf61	cis	cerebellum	SCAN
rs1546470	FOXN2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48445400-48450000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:48445800-48450000	Enhancers	Fetal Intestine Large	intestine
3	chr2:48446200-48450000	Enhancers	Fetal Intestine Small	intestine
4	chr2:48446800-48450800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:48447600-48450000	Enhancers	Liver	Liver
6	chr2:48448800-48449800	Enhancers	Hela-S3	cervix
7	chr2:48448800-48454000	Weak transcription	Primary B cells from cord blood	blood
8	chr2:48449000-48449800	Enhancers	Stomach Mucosa	stomach
9	chr2:48449200-48451200	Enhancers	HepG2	liver
10	chr2:48449200-48453000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:48449200-48454000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:48449400-48463400	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links