Variant report

Variant	rs2658954
Chromosome Location	chr12:45241770-45241771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10161447	0.84[EUR][1000 genomes]
rs10506258	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785535	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10785536	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785537	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785538	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785540	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11504491	0.81[EUR][1000 genomes]
rs11524561	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11615964	0.82[ASN][1000 genomes]
rs11833874	0.81[EUR][1000 genomes]
rs12316579	0.84[EUR][1000 genomes]
rs12818329	0.82[AMR][1000 genomes]
rs1376126	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1395397	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1506676	0.85[ASN][1000 genomes]
rs1506678	0.85[ASN][1000 genomes]
rs1506679	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1506680	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1605296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1605297	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1605298	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17095127	0.81[EUR][1000 genomes]
rs1857927	0.99[EUR][1000 genomes]
rs1876241	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055675	0.84[EUR][1000 genomes]
rs2055676	0.84[EUR][1000 genomes]
rs2055677	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2258058	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408083	0.81[EUR][1000 genomes]
rs2408084	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2408085	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2465108	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465109	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2465110	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2658948	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2658951	0.98[EUR][1000 genomes]
rs2658957	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2658959	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2658965	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2658966	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710453	0.99[EUR][1000 genomes]
rs2710455	0.84[EUR][1000 genomes]
rs2710457	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710459	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710460	0.84[EUR][1000 genomes]
rs2710461	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2710462	0.81[EUR][1000 genomes]
rs2939697	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2939698	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4238095	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4300447	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4499065	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4768075	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768577	0.84[EUR][1000 genomes]
rs55741117	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57190502	0.83[AMR][1000 genomes]
rs7295923	0.81[ASN][1000 genomes]
rs7304472	0.82[ASN][1000 genomes]
rs7312377	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74079970	0.81[EUR][1000 genomes]
rs7952764	0.85[ASN][1000 genomes]
rs7971834	0.81[EUR][1000 genomes]
rs7973268	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7979717	0.84[ASN][1000 genomes]
rs884259	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs884260	0.84[AMR][1000 genomes];1.00[EUR][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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45220600-45242000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:45221800-45242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:45230000-45242200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:45233600-45242000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr12:45234800-45242000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:45238400-45242000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45238400-45242000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:45239800-45241800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:45239800-45242000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:45240200-45248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:45240600-45242800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:45240800-45241800	Enhancers	GM12878-XiMat	blood
13	chr12:45240800-45242400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr12:45240800-45242400	Enhancers	Thymus	Thymus
15	chr12:45240800-45242800	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:45241000-45241800	Weak transcription	Fetal Brain Male	brain
17	chr12:45241000-45242000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:45241000-45242000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:45241000-45242200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:45241000-45245200	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:45241200-45242200	Weak transcription	Fetal Brain Female	brain
22	chr12:45241400-45242800	Flanking Active TSS	Dnd41	blood
23	chr12:45241600-45241800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr12:45241600-45242000	Active TSS	Primary T cells from cord blood	blood
25	chr12:45241600-45242000	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:45241600-45242400	Enhancers	Fetal Thymus	thymus
27	chr12:45241600-45242600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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