Variant report

Variant	rs6884138
Chromosome Location	chr5:92965213-92965214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10038831	0.86[JPT][hapmap]
rs10041792	0.86[JPT][hapmap]
rs1004941	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs10050364	0.85[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10060331	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs10067541	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs10071040	0.86[JPT][hapmap]
rs1031424	0.82[JPT][hapmap]
rs1038686	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1046217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10476520	0.86[JPT][hapmap]
rs10514376	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12186878	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs13154650	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs13155452	0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs13156202	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs13161885	0.86[JPT][hapmap]
rs13164315	0.86[JPT][hapmap]
rs13357713	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1453003	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1470150	0.87[CHD][hapmap]
rs17083264	0.87[EUR][1000 genomes]
rs17083278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17083280	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17083297	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17083377	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17312456	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17372615	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs17372649	0.86[JPT][hapmap]
rs17372725	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs1844343	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1982439	0.86[JPT][hapmap]
rs2924374	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs3776601	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56069221	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56259161	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57924239	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58143801	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58237393	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58919600	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59544418	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60553989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60827958	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61110137	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61429325	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556828	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556829	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556834	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6877616	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6879620	0.86[JPT][hapmap]
rs6881815	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6890998	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6892853	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6895356	0.86[JPT][hapmap]
rs6898507	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs73135334	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135354	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135367	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135371	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135373	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73135374	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135376	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135377	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7702348	0.86[JPT][hapmap]
rs7702649	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7704972	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7710106	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7713956	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7717718	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs7721168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731223	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7736624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9314086	0.87[CHD][hapmap];0.86[JPT][hapmap]

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	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6884138	ANKRD32	cis	cerebellum	SCAN
rs6884138	MAGOHB	trans	cerebellum	SCAN
rs6884138	CETN3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92957800-92970200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:92958400-92970400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:92959400-92969800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:92961400-93007000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:92965200-92985400	Weak transcription	Primary B cells from cord blood	blood

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