Variant report

Variant	rs1396826
Chromosome Location	chr2:48443754-48443755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48431668..48433629-chr2:48442154..48444145,2	MCF-7	breast:
2	chr2:48442344..48444202-chr2:48446205..48448068,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1112259	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11695011	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11899562	0.86[EUR][1000 genomes]
rs12469811	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621844	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713006	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13010470	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1546470	0.98[ASN][1000 genomes]
rs1546472	0.82[ASN][1000 genomes]
rs1567397	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2175138	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2348719	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348720	0.81[ASN][1000 genomes]
rs2348723	1.00[ASN][1000 genomes]
rs2348724	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2882004	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4375916	1.00[ASN][1000 genomes]
rs4953559	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953560	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953561	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4953567	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6545024	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6705995	0.96[ASN][1000 genomes]
rs6742830	0.98[ASN][1000 genomes]
rs6750123	0.81[AMR][1000 genomes]
rs6751603	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6755968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7583634	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7596628	0.81[ASN][1000 genomes]
rs876871	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs883795	0.83[EUR][1000 genomes]
rs906857	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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
rs1396826	FOXN2	cis	cerebellum	SCAN
rs1396826	FOXN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48437000-48446800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:48441600-48446600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links