Variant report

Variant	rs16878999
Chromosome Location	chr6:88029197-88029198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr6:88028957-88029262	K562	blood:	n/a	chr6:88029062-88029070
2	GATA3	chr6:88028996-88029689	SH-SY5Y	brain:	n/a	chr6:88029056-88029077 chr6:88029059-88029070

Variant related genes	Relation type
ENSG00000226524	TF binding region
SMIM8	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10484884	1.00[MEX][hapmap]
rs10488045	0.95[YRI][hapmap]
rs10498960	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes]
rs1359982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16878473	1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap]
rs16878570	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs16878622	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs16878638	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap]
rs16878712	0.95[YRI][hapmap]
rs16878713	0.95[YRI][hapmap]
rs16878734	0.82[AFR][1000 genomes]
rs16878736	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs16878809	0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs16878856	0.94[AFR][1000 genomes]
rs16878863	0.94[AFR][1000 genomes]
rs16878942	0.95[YRI][hapmap];1.00[AFR][1000 genomes]
rs16878991	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16879012	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16879089	1.00[MEX][hapmap]
rs16879117	1.00[MEX][hapmap]
rs16879144	1.00[MEX][hapmap]
rs1925693	1.00[MKK][hapmap];0.90[YRI][hapmap]
rs41273281	0.94[AFR][1000 genomes]
rs41273283	0.94[AFR][1000 genomes]
rs41397850	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap]
rs41398947	0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap]
rs45620640	0.90[EUR][1000 genomes]
rs56010354	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56193950	0.90[AFR][1000 genomes]
rs56305030	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56678817	0.81[AFR][1000 genomes]
rs56957450	0.90[EUR][1000 genomes]
rs57043501	1.00[AFR][1000 genomes]
rs57552196	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57596999	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57631457	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58321177	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58327183	0.87[AFR][1000 genomes]
rs58646133	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58731649	1.00[AFR][1000 genomes]
rs59127357	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59150116	0.91[AFR][1000 genomes]
rs59597706	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60544317	0.94[AFR][1000 genomes]
rs60628059	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60845773	0.91[AFR][1000 genomes]
rs61174011	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61705669	0.91[AFR][1000 genomes]
rs6454604	1.00[GIH][hapmap]
rs73483799	0.82[AFR][1000 genomes]
rs73485808	0.82[AFR][1000 genomes]
rs73485811	0.82[AFR][1000 genomes]
rs73485820	0.91[AFR][1000 genomes]
rs73485826	0.90[AFR][1000 genomes]
rs73485828	0.88[AFR][1000 genomes]
rs73485831	0.88[AFR][1000 genomes]
rs73488008	0.85[EUR][1000 genomes]
rs73488017	1.00[EUR][1000 genomes]
rs73488048	0.90[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16878999	SEMA5A	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88024200-88031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:88029000-88029800	Enhancers	K562	blood

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