Variant report

Variant	rs12728111
Chromosome Location	chr1:63346572-63346573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10159426	0.84[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs10493327	0.94[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10749735	0.86[EUR][1000 genomes]
rs10889383	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10889384	0.82[ASN][1000 genomes]
rs10889385	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10889386	0.89[JPT][hapmap]
rs10889387	0.89[ASN][1000 genomes]
rs11208032	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11208035	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11208036	0.86[EUR][1000 genomes]
rs11208037	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208038	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208040	0.96[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208043	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11208045	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11208046	0.96[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11208047	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208049	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11208050	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11208051	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11208052	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11208056	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11579171	0.81[EUR][1000 genomes]
rs11579518	0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11580642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584363	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587081	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803404	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11804568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12120847	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12128286	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12129919	0.85[EUR][1000 genomes]
rs12134455	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12564421	0.84[ASN][1000 genomes]
rs12567999	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12725996	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12742537	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743698	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12748640	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12749904	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12750156	0.80[EUR][1000 genomes]
rs12752360	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12756081	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333730	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1333733	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1333734	0.89[ASN][1000 genomes]
rs1333736	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1360677	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs1360678	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1413242	0.86[ASN][1000 genomes]
rs1537496	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17097064	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1931079	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1981067	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050248	0.85[ASN][1000 genomes]
rs2366820	0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2366821	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2366822	0.82[ASN][1000 genomes]
rs2803238	0.89[CHB][hapmap]
rs2886770	0.89[JPT][hapmap]
rs2886771	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3211074	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs3737892	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737893	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4396149	0.83[EUR][1000 genomes]
rs4448545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587990	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587991	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6587992	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587993	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587994	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587996	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6587997	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587998	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656119	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657235	0.85[EUR][1000 genomes]
rs6657552	0.89[ASN][1000 genomes]
rs6657707	0.91[EUR][1000 genomes]
rs6660873	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663165	0.82[ASN][1000 genomes]
rs6665932	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6670072	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670694	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676637	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6676821	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6677051	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679582	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6682286	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6683423	0.83[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs6683732	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683832	0.89[JPT][hapmap]
rs6685784	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686232	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6687943	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6693530	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695607	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6699457	0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7512374	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7512480	0.95[CHB][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs7512529	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7513520	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7515960	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519205	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7521483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522726	0.87[ASN][1000 genomes]
rs7524508	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7526246	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527423	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7527905	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7531329	0.84[ASN][1000 genomes]
rs7535496	0.93[ASN][1000 genomes]
rs7540030	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs7540205	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553110	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7555606	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs998096	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830015	chr1:63261143-63455296	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12728111	ATG4C	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63342400-63347000	Weak transcription	Brain Germinal Matrix	brain
2	chr1:63343000-63347000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:63345800-63348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:63346200-63347000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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