Variant report

Variant	rs884259
Chromosome Location	chr12:45253662-45253663
allele	G/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:63)

rs_ID	r²[population]
rs10161447	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10506258	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10785535	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10785536	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785537	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785538	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785540	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11504491	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11524561	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833874	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12316579	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1376126	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1395397	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1506679	0.93[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1506680	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1605296	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1605297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1605298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17095127	0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1857927	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1876241	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2055675	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2055676	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2055677	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2258058	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408083	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2408084	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408085	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465108	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2465110	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2658948	0.92[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2658951	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2658954	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2658957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658959	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2658966	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710453	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2710455	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2710457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2710459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710460	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2710461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710462	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2939697	0.87[AFR][1000 genomes]
rs2939698	0.87[AFR][1000 genomes]
rs4238095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4300447	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4415832	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes]
rs4499065	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4768075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768577	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768578	0.81[AMR][1000 genomes]
rs55741117	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7312377	0.86[EUR][1000 genomes]
rs74079970	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7957052	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs7957160	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs7960817	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs7971834	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7973268	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs884260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45248600-45259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:45248800-45255800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr12:45249000-45255400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr12:45250600-45253800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:45250800-45255400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:45252200-45255600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:45252400-45253800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:45252400-45255200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:45252800-45254200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:45252800-45255000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:45253400-45253800	Enhancers	Primary T cells from cord blood	blood
12	chr12:45253600-45255000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:45253600-45255400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:45253600-45258200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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