Variant report

Variant	rs56989457
Chromosome Location	chr12:45096893-45096894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11182615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1450555	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1450556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1869163	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57533444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57804181	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59161217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60629070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60933400	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7131850	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7133504	1.00[AMR][1000 genomes]
rs7134991	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7295485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7301727	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7954476	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7954828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7957686	0.89[AMR][1000 genomes]
rs7959316	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965285	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7966932	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7974610	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9739530	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45065000-45116000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45080800-45136000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:45081400-45115600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:45081600-45106800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45081800-45103000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:45083200-45110000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:45085400-45101000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:45085400-45105800	Weak transcription	Fetal Brain Female	brain
9	chr12:45088000-45110800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:45089000-45114200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:45089600-45106400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:45090600-45110200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:45091200-45110800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:45093200-45099800	Weak transcription	Fetal Brain Male	brain
15	chr12:45094000-45102200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:45095600-45097600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:45096600-45097400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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