Variant report

Variant	rs2471403
Chromosome Location	chr2:48490508-48490509
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	chr2:48487519..48489450-chr2:48489934..48492138,2	K562	blood:
2	chr14:81611696..81613196-chr2:48488940..48490546,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10153773	0.82[JPT][hapmap]
rs10186237	0.88[YRI][hapmap]
rs10199431	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs11676168	0.89[GIH][hapmap]
rs11682044	0.80[GIH][hapmap];0.88[YRI][hapmap]
rs11685861	0.88[YRI][hapmap]
rs11690690	0.88[YRI][hapmap]
rs12616792	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713008	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13386751	0.89[AFR][1000 genomes]
rs13388291	0.83[JPT][hapmap]
rs13426834	0.87[AFR][1000 genomes]
rs13432998	0.91[GIH][hapmap]
rs2471404	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471405	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28806843	0.80[AFR][1000 genomes]
rs4411759	0.82[JPT][hapmap]
rs4547573	0.91[JPT][hapmap];0.84[YRI][hapmap]
rs60677957	0.83[AFR][1000 genomes]
rs62138801	0.80[AFR][1000 genomes]
rs6545026	0.88[YRI][hapmap]
rs6545027	0.88[YRI][hapmap]
rs6545030	0.88[YRI][hapmap]
rs6545036	0.92[YRI][hapmap]
rs6705802	0.84[YRI][hapmap]
rs6712029	0.88[YRI][hapmap]
rs7340322	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7566239	0.92[YRI][hapmap]
rs7568960	0.90[AFR][1000 genomes]
rs7576964	0.88[YRI][hapmap]
rs7577237	0.92[YRI][hapmap]
rs7579932	0.92[YRI][hapmap]
rs7600794	0.87[YRI][hapmap]
rs7606104	0.88[YRI][hapmap]

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
rs2471403	SOCS5	cis	parietal	SCAN
rs2471403	EPAS1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48482000-48491400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:48486600-48492200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:48487200-48492000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:48488400-48491800	Enhancers	K562	blood
5	chr2:48490000-48490600	Bivalent Enhancer	HepG2	liver

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