Variant report

Variant	rs884584
Chromosome Location	chr15:39943041-39943042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39936644..39939290-chr15:39941408..39943879,2	K562	blood:
2	chr15:39940443..39943300-chr15:39951090..39953901,2	MCF-7	breast:

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs1004740	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs10152640	0.83[CHD][hapmap]
rs10520135	0.87[CEU][hapmap]
rs10520137	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10520142	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11070220	1.00[CEU][hapmap]
rs11070221	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070222	1.00[CEU][hapmap];0.80[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070223	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070224	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070225	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070226	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070227	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070228	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1134485	1.00[CEU][hapmap]
rs11630406	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631570	1.00[CEU][hapmap]
rs11632117	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633974	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs11635103	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636823	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638041	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11638500	1.00[CEU][hapmap]
rs11638558	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852591	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11854797	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs11855487	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11856294	1.00[CEU][hapmap]
rs11856971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857819	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11857927	1.00[CEU][hapmap]
rs12443011	0.83[CHD][hapmap]
rs12899323	0.94[EUR][1000 genomes]
rs12901142	0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12903514	0.93[EUR][1000 genomes]
rs12908846	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911549	0.95[EUR][1000 genomes]
rs12912082	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[TSI][hapmap]
rs16969386	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969395	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16969410	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16969426	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16969429	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16969445	1.00[CEU][hapmap]
rs16969451	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16969459	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16969460	1.00[CEU][hapmap]
rs16969475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969478	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969637	1.00[MEX][hapmap]
rs16969640	0.89[MEX][hapmap]
rs1876852	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1876853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228261	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[TSI][hapmap]
rs2292305	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs2411299	0.85[TSI][hapmap];0.95[EUR][1000 genomes]
rs2411308	0.91[EUR][1000 genomes]
rs2411309	0.93[EUR][1000 genomes]
rs2411311	0.95[EUR][1000 genomes]
rs2411313	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2411314	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2411315	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2412409	1.00[CEU][hapmap]
rs2412412	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2412413	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412414	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412415	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412416	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412418	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2412419	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2412420	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2412421	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2631700	0.86[EUR][1000 genomes]
rs28437905	0.93[EUR][1000 genomes]
rs2898685	0.94[EUR][1000 genomes]
rs2898686	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2898687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2898688	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898962	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3743125	0.87[TSI][hapmap]
rs3784390	1.00[CEU][hapmap]
rs4319740	0.88[ASN][1000 genomes]
rs4349120	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4476147	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4479205	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4480779	0.93[EUR][1000 genomes]
rs4526992	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547308	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4583211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4606692	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4628934	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56938133	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59449051	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60164392	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60195210	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61130460	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61439563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61568256	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492909	0.93[EUR][1000 genomes]
rs66781090	0.87[ASN][1000 genomes]
rs67239630	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7162070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162781	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167100	0.93[EUR][1000 genomes]
rs7167184	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168755	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169478	1.00[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7169574	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7170335	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7176721	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7177324	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7179293	0.81[JPT][hapmap]
rs7179608	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180675	0.92[ASN][1000 genomes]
rs72725079	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72725080	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72725084	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72725093	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72725101	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753599	1.00[CEU][hapmap]
rs8026916	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029602	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8032035	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8032289	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8033902	0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs8034594	0.80[CHB][hapmap]
rs8034885	0.89[EUR][1000 genomes]
rs8036226	0.93[EUR][1000 genomes]
rs8036376	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs8036633	0.88[CEU][hapmap]
rs8042068	0.95[EUR][1000 genomes]
rs9302102	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs949646	0.85[JPT][hapmap]
rs9672572	0.86[EUR][1000 genomes]
rs9806365	0.92[ASN][1000 genomes]
rs9806647	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999393	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs884584	THBS1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39937800-39943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:39938000-39944400	Weak transcription	HSMMtube	muscle
3	chr15:39938000-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:39938200-39950800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:39942800-39943400	Enhancers	Left Ventricle	heart

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