Variant report

Variant	rs7557630
Chromosome Location	chr2:56225534-56225535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10171335	1.00[ASN][1000 genomes]
rs1017371	0.90[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10194204	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194401	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200414	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206522	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206619	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210936	1.00[ASN][1000 genomes]
rs11686318	1.00[ASN][1000 genomes]
rs11690813	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11693755	1.00[ASN][1000 genomes]
rs11891825	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11893449	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11903947	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11904173	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12713312	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713313	1.00[ASN][1000 genomes]
rs12713314	1.00[ASN][1000 genomes]
rs12991457	1.00[ASN][1000 genomes]
rs13029542	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13398053	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399945	1.00[ASN][1000 genomes]
rs13410155	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431392	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432828	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347093	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1432553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1835897	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868992	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34561537	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4553860	1.00[ASN][1000 genomes]
rs4999828	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6545535	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6545536	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545537	0.90[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545538	0.90[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545539	0.94[ASN][1000 genomes]
rs6724635	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724872	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741589	1.00[ASN][1000 genomes]
rs6745615	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756818	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587002	1.00[ASN][1000 genomes]
rs7597360	1.00[ASN][1000 genomes]
rs7601814	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967780	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7557630	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56220400-56225800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr2:56222000-56226000	Weak transcription	Osteobl	bone
3	chr2:56222000-56229600	Weak transcription	Fetal Stomach	stomach
4	chr2:56222400-56226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56223000-56226000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:56225200-56225600	Enhancers	HUVEC	blood vessel
7	chr2:56225400-56226000	Enhancers	Hela-S3	cervix

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