Variant report

Variant	rs4887125
Chromosome Location	chr15:74559478-74559479
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12441994	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1484213	0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs16967313	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843366	0.81[ASN][1000 genomes]
rs189499	0.81[TSI][hapmap]
rs191589	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs28395230	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2930296	0.81[EUR][1000 genomes]
rs2930297	0.83[EUR][1000 genomes]
rs2930848	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2930849	0.83[EUR][1000 genomes]
rs2959013	0.83[EUR][1000 genomes]
rs2959014	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2959015	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2959016	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs351199	0.84[EUR][1000 genomes]
rs351201	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs351204	0.80[EUR][1000 genomes]
rs351207	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs351209	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs351210	0.80[EUR][1000 genomes]
rs351211	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs351214	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs351215	0.80[EUR][1000 genomes]
rs4886593	0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4887123	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4887124	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57622624	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61182982	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61653296	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7163055	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73434405	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs735980	0.83[JPT][hapmap];0.90[LWK][hapmap]
rs901133	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs94899	0.80[CHB][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][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	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1035367	chr15:74554972-74586538	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4887125	NPTN	cis	lymphoblastoid	seeQTL
rs4887125	RPLP1	cis	parietal	SCAN
rs4887125	SCAMP5	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74557000-74560000	Weak transcription	Spleen	Spleen
2	chr15:74557000-74561000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:74557600-74563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:74557800-74563200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:74557800-74570400	Weak transcription	Fetal Brain Male	brain
6	chr15:74558000-74563400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:74558600-74562000	Weak transcription	Fetal Brain Female	brain

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