Variant report

Variant	rs7574684
Chromosome Location	chr2:100992912-100992913
allele	C/T
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	SPI1	chr2:100992775-100993305	HL-60	blood:	n/a	n/a
2	SPI1	chr2:100992817-100993326	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000270699	TF binding region

Extended variants
information (count: 122 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10167159	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10180570	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10184899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198495	0.88[ASN][1000 genomes]
rs10198682	0.88[ASN][1000 genomes]
rs10200480	0.88[ASN][1000 genomes]
rs10201098	0.88[ASN][1000 genomes]
rs10204833	0.88[ASN][1000 genomes]
rs10206374	1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208900	0.88[ASN][1000 genomes]
rs10208911	0.88[ASN][1000 genomes]
rs10209186	0.88[ASN][1000 genomes]
rs1057056	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1057063	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1107429	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124009	0.86[AMR][1000 genomes]
rs13391930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410582	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420942	0.88[ASN][1000 genomes]
rs1347721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1370627	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1437970	0.88[ASN][1000 genomes]
rs17023985	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024035	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17024136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024209	0.86[AMR][1000 genomes]
rs1898571	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898574	0.88[ASN][1000 genomes]
rs2309793	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748936	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4149506	0.81[AMR][1000 genomes]
rs4149509	0.81[AMR][1000 genomes]
rs4149514	0.83[AMR][1000 genomes]
rs4149515	0.86[AMR][1000 genomes]
rs55640826	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55843950	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051859	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56118658	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56342384	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56656536	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56741959	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57862179	0.83[AMR][1000 genomes]
rs58164864	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58876304	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60131548	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60609848	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60898093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61321970	0.88[ASN][1000 genomes]
rs61710328	0.83[AMR][1000 genomes]
rs6542931	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542932	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542939	0.88[ASN][1000 genomes]
rs6542941	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6708942	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6713862	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714109	0.88[ASN][1000 genomes]
rs6716009	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716367	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6724695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725672	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6732285	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736938	0.81[AMR][1000 genomes]
rs6739576	0.88[ASN][1000 genomes]
rs6739589	0.90[AMR][1000 genomes]
rs6740098	0.88[ASN][1000 genomes]
rs6749572	0.81[AMR][1000 genomes]
rs6750866	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754379	0.88[ASN][1000 genomes]
rs6754869	0.83[AMR][1000 genomes]
rs6755285	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6755395	0.88[ASN][1000 genomes]
rs6757774	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758156	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758161	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758515	1.00[ASN][1000 genomes]
rs6758622	0.83[AMR][1000 genomes]
rs6761561	1.00[ASN][1000 genomes]
rs72960172	0.88[ASN][1000 genomes]
rs72960184	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960202	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73966107	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73966108	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73968412	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73968415	0.82[ASN][1000 genomes]
rs73968817	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556717	0.88[ASN][1000 genomes]
rs7557137	0.88[ASN][1000 genomes]
rs7559939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559946	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561065	0.81[AMR][1000 genomes]
rs7562461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562479	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562486	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564178	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7572119	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7576749	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582096	0.81[AMR][1000 genomes]
rs7582546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585713	0.81[AMR][1000 genomes]
rs7585898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587333	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7596483	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7597631	0.88[ASN][1000 genomes]
rs7597722	0.88[ASN][1000 genomes]
rs7606723	0.88[ASN][1000 genomes]
rs9308834	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv874701	chr2:100976139-101023261	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7574684	NPAS4	trans	brain	seeQTL
rs7574684	FOSB	trans	brain	seeQTL
rs7574684	EGR2	trans	brain	seeQTL
rs7574684	FOS	trans	brain	seeQTL
rs7574684	ARC	trans	brain	seeQTL
rs7574684	EGR4	trans	brain	seeQTL
rs7574684	DUSP2	trans	brain	seeQTL
rs7574684	PTGS2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100992800-100993200	Enhancers	Primary monocytes fromperipheralblood	blood

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