Variant report

Variant	rs4075052
Chromosome Location	chr16:31348233-31348234
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31342392..31343986-chr16:31347244..31349142,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10747210	0.92[ASN][1000 genomes]
rs10782004	0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1106398	0.93[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11150610	0.93[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11150611	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11150612	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11150613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11150614	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11150616	0.90[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11150619	0.90[JPT][hapmap]
rs1143682	0.93[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11574630	0.93[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11574631	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11574639	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11641202	0.82[CHD][hapmap];0.91[ASN][1000 genomes]
rs11641624	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs11642120	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11645526	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs11645917	0.94[ASN][1000 genomes]
rs11859274	0.94[ASN][1000 genomes]
rs11863627	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12597154	0.93[ASN][1000 genomes]
rs12600286	0.87[ASN][1000 genomes]
rs12923297	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12935192	0.94[ASN][1000 genomes]
rs13332545	0.95[JPT][hapmap]
rs13338928	0.95[ASN][1000 genomes]
rs2011491	0.83[EUR][1000 genomes]
rs2359661	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs28372932	0.93[ASN][1000 genomes]
rs3087796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36100148	0.96[ASN][1000 genomes]
rs3764327	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3815801	0.86[CHB][hapmap]
rs3925074	0.99[ASN][1000 genomes]
rs3925075	0.99[ASN][1000 genomes]
rs4077810	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41440449	0.93[ASN][1000 genomes]
rs4261553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280256	0.85[ASN][1000 genomes]
rs4359460	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411512	0.98[ASN][1000 genomes]
rs4448960	0.99[ASN][1000 genomes]
rs4450409	0.90[ASN][1000 genomes]
rs4459557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4493054	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4506917	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4525506	0.81[ASN][1000 genomes]
rs4594268	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597342	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4608351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889543	0.94[ASN][1000 genomes]
rs4889640	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs4889647	0.90[ASN][1000 genomes]
rs4889649	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs55742763	0.94[ASN][1000 genomes]
rs55912556	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56392848	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57202326	0.90[ASN][1000 genomes]
rs59338016	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61194152	0.92[ASN][1000 genomes]
rs62051517	0.96[ASN][1000 genomes]
rs6565225	0.85[EUR][1000 genomes]
rs7190997	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7192161	0.90[ASN][1000 genomes]
rs7192375	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7193943	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7195915	0.96[ASN][1000 genomes]
rs7195945	0.96[ASN][1000 genomes]
rs7203472	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7206295	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7499192	0.86[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7501207	0.87[ASN][1000 genomes]
rs8048583	0.93[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs8052324	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057320	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs8058882	0.91[ASN][1000 genomes]
rs8060268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8062159	0.91[ASN][1000 genomes]
rs929868	0.83[EUR][1000 genomes]
rs9673398	0.98[ASN][1000 genomes]
rs9673404	0.97[ASN][1000 genomes]
rs9673405	0.99[ASN][1000 genomes]
rs9673519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673522	0.99[ASN][1000 genomes]
rs9674009	0.99[ASN][1000 genomes]
rs9888907	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4075052	ITGAX	cis	multi-tissue	Pritchard
rs4075052	MYST1	cis	cerebellum	SCAN
rs4075052	VKORC1	cis	cerebellum	SCAN
rs4075052	ITGAM	cis	multi-tissue	Pritchard
rs4075052	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx
rs4075052	MYST1	cis	parietal	SCAN
rs4075052	ITGAM	cis	Liver	GTEx
rs4075052	FUS	cis	cerebellum	SCAN
rs4075052	ITGAX	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31345600-31349200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr16:31345600-31349200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:31345600-31349400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr16:31345800-31350200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:31348000-31348800	Active TSS	Spleen	Spleen

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