Variant report

Variant	rs3925075
Chromosome Location	chr16:31347748-31347749
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	chr16:30999038..31001529-chr16:31346351..31348185,2	K562	blood:
2	chr16:31342392..31343986-chr16:31347244..31349142,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10747210	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782004	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1106398	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11150610	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11150611	0.94[ASN][1000 genomes]
rs11150612	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs11150613	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11150614	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11150616	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11150619	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs1143682	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11574630	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11574631	0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11641202	0.90[CHD][hapmap];0.90[GIH][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11642120	0.92[ASN][1000 genomes]
rs11645917	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11859274	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11863627	0.91[ASN][1000 genomes]
rs12597154	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12600286	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12923297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12935192	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13332545	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13338928	0.94[ASN][1000 genomes]
rs2359661	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap]
rs28372932	0.94[ASN][1000 genomes]
rs3087796	0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs36100148	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3925074	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075052	0.99[ASN][1000 genomes]
rs4077810	0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs41440449	0.94[ASN][1000 genomes]
rs4261553	0.99[ASN][1000 genomes]
rs4280256	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4359460	0.99[ASN][1000 genomes]
rs4411512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4448960	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450409	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4459557	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4493054	0.92[ASN][1000 genomes]
rs4506917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525506	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4594268	0.92[ASN][1000 genomes]
rs4597342	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4608351	0.99[ASN][1000 genomes]
rs4889543	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889647	0.91[ASN][1000 genomes]
rs4889649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55742763	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55912556	0.84[ASN][1000 genomes]
rs56392848	0.94[ASN][1000 genomes]
rs57202326	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59338016	0.95[ASN][1000 genomes]
rs61194152	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62051517	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7190997	0.90[JPT][hapmap]
rs7192161	0.91[ASN][1000 genomes]
rs7192375	0.94[ASN][1000 genomes]
rs7195915	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7195945	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206295	0.93[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7499192	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7501207	0.87[ASN][1000 genomes]
rs8044482	0.80[AMR][1000 genomes]
rs8048583	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8052324	0.92[ASN][1000 genomes]
rs8058882	0.92[ASN][1000 genomes]
rs8060268	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs8062159	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9673398	0.99[ASN][1000 genomes]
rs9673404	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9673405	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9673522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9674009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888907	0.99[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

Variant related diseases (count:1)

Disease	PMID	Source
IgA nephropathy	22197929	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3925075	ITGAM	cis	lymphoblastoid	seeQTL
rs3925075	ITGAX	cis	lymphoblastoid	seeQTL
rs3925075	MYST1	cis	cerebellum	SCAN
rs3925075	RABEP2	cis	cerebellum	SCAN
rs3925075	ITGAX	cis	multi-tissue	Pritchard

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	chr16:31344000-31348000	Weak transcription	Spleen	Spleen
3	chr16:31345600-31349200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr16:31345600-31349200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr16:31345600-31349400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:31345800-31350200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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