Variant report

Variant	rs12306215
Chromosome Location	chr12:120041481-120041482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10774503	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774508	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10849675	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849676	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849680	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064844	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064845	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064846	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11064847	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11064849	0.80[AMR][1000 genomes]
rs11064850	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1109855	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1109857	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	0.88[CEU][hapmap]
rs1985743	0.82[AMR][1000 genomes]
rs2393522	0.86[EUR][1000 genomes]
rs2393523	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2393524	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs278123	0.88[CEU][hapmap]
rs278143	0.88[CEU][hapmap]
rs278144	0.87[CEU][hapmap]
rs278145	0.88[CEU][hapmap]
rs278147	0.88[CEU][hapmap]
rs278148	0.88[CEU][hapmap]
rs278149	0.88[CEU][hapmap]
rs278151	0.88[CEU][hapmap]
rs278152	0.88[CEU][hapmap]
rs278155	0.88[CEU][hapmap]
rs34500179	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4213	0.88[CEU][hapmap]
rs6490259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138221	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7138756	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7301592	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304294	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310148	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310536	0.86[EUR][1000 genomes]
rs7311445	0.82[EUR][1000 genomes]
rs7311779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739421	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739422	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952841	0.82[AMR][1000 genomes]
rs7955119	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7963332	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972445	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7973772	0.82[AMR][1000 genomes]
rs7978755	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970095	0.80[GIH][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916688	chr12:119801814-120044407	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv832529	chr12:119863378-120071646	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12306215	PXN	cis	cerebellum	SCAN
rs12306215	WSB2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120034600-120048200	Weak transcription	HSMMtube	muscle
2	chr12:120036600-120046000	Weak transcription	HSMM	muscle
3	chr12:120036600-120049000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:120040200-120042400	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr12:120040200-120042600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr12:120040400-120042000	Enhancers	Psoas Muscle	Psoas
7	chr12:120041200-120041600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:120041400-120041600	Enhancers	Gastric	stomach
9	chr12:120041400-120041800	Enhancers	Liver	Liver

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