Variant report

Variant	rs2253649
Chromosome Location	chr1:223462821-223462822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1019278	1.00[AMR][1000 genomes]
rs11488546	1.00[AMR][1000 genomes]
rs1341287	1.00[AMR][1000 genomes]
rs1341288	1.00[EUR][1000 genomes]
rs1417744	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1640803	1.00[MEX][hapmap]
rs1713218	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17518279	0.85[YRI][hapmap]
rs1856932	1.00[EUR][1000 genomes]
rs2487832	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793466	1.00[EUR][1000 genomes]
rs28584917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3768284	1.00[MEX][hapmap]
rs5744122	1.00[MEX][hapmap]
rs5744162	1.00[AMR][1000 genomes]
rs5744167	1.00[MEX][hapmap]
rs61737415	1.00[AMR][1000 genomes]
rs73115888	1.00[AMR][1000 genomes]
rs73118103	1.00[AMR][1000 genomes]
rs73118104	1.00[AMR][1000 genomes]
rs73118106	1.00[AMR][1000 genomes]
rs73118108	1.00[AMR][1000 genomes]
rs73118111	1.00[AMR][1000 genomes]
rs73118118	1.00[AMR][1000 genomes]
rs73118120	1.00[AMR][1000 genomes]
rs73118121	1.00[AMR][1000 genomes]
rs73120209	1.00[AMR][1000 genomes]
rs73120240	1.00[AMR][1000 genomes]
rs73120248	1.00[AMR][1000 genomes]
rs73120252	1.00[AMR][1000 genomes]
rs73120270	1.00[AMR][1000 genomes]
rs73120271	1.00[AMR][1000 genomes]
rs73120274	1.00[AMR][1000 genomes]
rs73120283	1.00[AMR][1000 genomes]
rs73120288	1.00[AMR][1000 genomes]
rs73122203	1.00[AMR][1000 genomes]
rs73122204	1.00[AMR][1000 genomes]
rs73122205	1.00[AMR][1000 genomes]
rs73122207	1.00[AMR][1000 genomes]
rs73122216	1.00[AMR][1000 genomes]
rs73122222	1.00[AMR][1000 genomes]
rs73122236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122238	1.00[EUR][1000 genomes]
rs73122239	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124222	1.00[AMR][1000 genomes]
rs825119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs825121	1.00[EUR][1000 genomes]
rs825122	1.00[EUR][1000 genomes]
rs825126	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs851140	1.00[MEX][hapmap]
rs851151	1.00[MEX][hapmap]
rs851195	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs851197	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs851200	0.89[ASW][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2253649	CAPN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223440800-223465600	Weak transcription	Ovary	ovary
2	chr1:223443800-223472600	Weak transcription	Gastric	stomach
3	chr1:223459000-223474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:223460800-223473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:223461200-223469600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:223462600-223465600	Weak transcription	Primary T cells from cord blood	blood

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