Variant report

Variant	rs2408047
Chromosome Location	chr12:45135052-45135053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10748401	0.91[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10748402	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10785518	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10785520	0.82[ASW][hapmap];0.91[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785521	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785522	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10785523	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10785524	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10785525	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10785526	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785527	0.91[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880665	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10880667	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880668	0.91[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880669	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880670	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880671	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880672	0.91[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880674	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880675	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10880676	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11182562	0.85[CHB][hapmap]
rs12302273	0.84[EUR][1000 genomes]
rs1450540	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1450551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1470803	0.82[ASW][hapmap];0.83[CEU][hapmap]
rs17094882	0.88[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs1711839	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060898	0.83[CEU][hapmap]
rs2060899	0.82[CEU][hapmap]
rs2084614	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2218943	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs2408048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768569	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs586188	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs590905	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs617006	0.91[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]
rs625691	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs632893	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs633526	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs641782	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs655191	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6582514	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582515	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs683285	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs686110	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7299592	0.84[EUR][1000 genomes]
rs7304431	0.82[ASW][hapmap];0.83[CEU][hapmap]
rs765770	0.82[CEU][hapmap]
rs838975	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1049080	chr12:45097564-45195295	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	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
5	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:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45080800-45136000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:45123400-45142400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:45127400-45136800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:45133600-45135200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45134400-45143400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:45134400-45165200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:45134600-45135200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:45134800-45135400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:45134800-45141400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:45135000-45135400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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