Variant report

Variant	rs12592914
Chromosome Location	chr15:54894829-54894830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10220855	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632253	0.96[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11632366	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11852743	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs12592900	0.92[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12708436	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1520411	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs1818704	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1818711	0.88[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1850994	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1851000	0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1851003	1.00[YRI][hapmap]
rs1851005	0.95[CEU][hapmap]
rs1851010	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972137	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2250283	0.87[LWK][hapmap];0.95[YRI][hapmap]
rs2250692	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs2414327	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414330	0.91[YRI][hapmap]
rs2414331	0.88[CEU][hapmap]
rs2460603	0.91[YRI][hapmap]
rs2460604	0.82[LWK][hapmap];0.91[YRI][hapmap]
rs2460605	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2460606	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2460608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2553216	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2553217	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2553220	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553221	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553225	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2681958	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681959	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2681964	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2681965	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2681966	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2911846	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2911847	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2947001	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2947003	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35710610	0.84[ASN][1000 genomes]
rs3848141	0.92[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs3959676	0.84[CEU][hapmap]
rs6493694	0.85[EUR][1000 genomes]
rs6493695	0.86[EUR][1000 genomes]
rs7174529	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72740053	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9284299	0.96[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904237	chr15:54888537-54927484	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv569509	chr15:54888537-54932716	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv457154	chr15:54892583-54904782	Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv569517	chr15:54892583-54904782	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54893800-54895400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr15:54894400-54895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:54894400-54895200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:54894600-54896800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:54894600-54896800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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