Variant report

Variant	rs2554854
Chromosome Location	chr12:51260727-51260728
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10160844	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459237	0.93[ASN][1000 genomes]
rs10459238	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10459239	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747595	0.86[ASN][1000 genomes]
rs10747596	0.85[ASN][1000 genomes]
rs10747597	0.93[ASN][1000 genomes]
rs10747599	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783393	0.91[ASN][1000 genomes]
rs10783394	0.93[ASN][1000 genomes]
rs10783395	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783404	0.91[ASN][1000 genomes]
rs10783406	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876099	0.93[ASN][1000 genomes]
rs10876100	0.92[ASN][1000 genomes]
rs10876105	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876115	0.93[ASN][1000 genomes]
rs10876119	0.90[ASN][1000 genomes]
rs1096030	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096031	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1103441	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169587	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169588	0.93[ASN][1000 genomes]
rs11169589	0.93[ASN][1000 genomes]
rs11169592	0.91[ASN][1000 genomes]
rs11169593	0.81[EUR][1000 genomes]
rs11169602	0.93[ASN][1000 genomes]
rs11169603	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169608	0.93[ASN][1000 genomes]
rs11169609	0.93[ASN][1000 genomes]
rs11169610	0.92[ASN][1000 genomes]
rs11169612	0.92[ASN][1000 genomes]
rs11495280	0.89[ASN][1000 genomes]
rs11533636	0.91[ASN][1000 genomes]
rs12578465	0.91[ASN][1000 genomes]
rs12578466	0.91[ASN][1000 genomes]
rs12581103	0.93[ASN][1000 genomes]
rs1362964	0.93[ASN][1000 genomes]
rs1583697	0.93[ASN][1000 genomes]
rs1631348	0.88[ASN][1000 genomes]
rs1642997	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1643004	0.96[ASN][1000 genomes]
rs1659375	0.93[ASN][1000 genomes]
rs2554852	0.94[ASN][1000 genomes]
rs3752667	0.93[ASN][1000 genomes]
rs4483656	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768926	0.91[ASN][1000 genomes]
rs4768937	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768938	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768939	0.93[ASN][1000 genomes]
rs7131969	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73100855	0.91[ASN][1000 genomes]
rs7979616	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829120	0.84[ASN][1000 genomes]
rs829122	0.91[ASN][1000 genomes]
rs829126	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs829128	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829129	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829139	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829141	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829142	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829143	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844175	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860476	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51259600-51260800	Enhancers	Esophagus	oesophagus
2	chr12:51260000-51260800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:51260200-51260800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr12:51260400-51260800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:51260400-51260800	Enhancers	Fetal Thymus	thymus
6	chr12:51260400-51261000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:51260400-51261000	Enhancers	Thymus	Thymus
8	chr12:51260600-51260800	Enhancers	Primary T cells from cord blood	blood
9	chr12:51260600-51260800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr12:51260600-51260800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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