Variant report

Variant	rs9888739
Chromosome Location	chr16:31313253-31313254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31212793..31214907-chr16:31311577..31313966,2	MCF-7	breast:
2	chr16:31306439..31308367-chr16:31312122..31314629,2	K562	blood:
3	chr16:31127178..31129343-chr16:31311883..31313531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103510	Chromatin interaction
ENSG00000261359	Chromatin interaction
ENSG00000103490	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11150615	1.00[ASN][1000 genomes]
rs1143678	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs1143679	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143683	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs11574636	1.00[ASN][1000 genomes]
rs11574637	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11641202	0.83[LWK][hapmap];0.91[YRI][hapmap]
rs11859300	1.00[ASN][1000 genomes]
rs11859349	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860650	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861161	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864503	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864541	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864813	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865746	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102768	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102791	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12103025	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917874	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12920597	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928725	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935156	0.81[EUR][1000 genomes]
rs13331557	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13338069	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28385574	1.00[ASN][1000 genomes]
rs28773820	1.00[ASN][1000 genomes]
rs28825532	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28834423	1.00[ASN][1000 genomes]
rs28855735	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082782	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34572943	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34767000	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34770440	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35314490	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383035	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35472514	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36001237	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055763	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41476751	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4548893	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4632147	1.00[ASN][1000 genomes]
rs58408589	1.00[ASN][1000 genomes]
rs59559257	1.00[ASN][1000 genomes]
rs60312440	1.00[ASN][1000 genomes]
rs6565227	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565228	0.85[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67898294	1.00[ASN][1000 genomes]
rs71389500	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71390269	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71391210	1.00[ASN][1000 genomes]
rs7184339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184677	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187713	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190018	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190807	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192039	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193268	0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs7198598	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199496	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199532	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200615	1.00[ASN][1000 genomes]
rs7204735	1.00[ASN][1000 genomes]
rs7206312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73534420	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7499077	1.00[CHD][hapmap]
rs8056276	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056944	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9745421	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9922766	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923357	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928372	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930524	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933520	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs9933937	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936831	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937645	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937837	1.00[CHD][hapmap]
rs9938063	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939679	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940397	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1817837	chr16:31301125-31331958	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	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

Variant related diseases (count:3)

Disease	PMID	Source
Systemic lupus erythematosus	18204446	GWAS catalog
Systemic lupus erythematosus	24871463	GWAS catalog
Systemic lupus erythematosus	21408207	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9888739	FAM57B	cis	parietal	SCAN
rs9888739	PYCARD	cis	lymphoblastoid	seeQTL
rs9888739	ITGAM	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31304600-31313400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr16:31306600-31313800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31310200-31326800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:31312600-31313800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr16:31312800-31313600	Enhancers	Primary hematopoietic stem cells	blood
6	chr16:31312800-31313800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr16:31313000-31313600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr16:31313000-31313800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr16:31313000-31314600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr16:31313200-31313400	Enhancers	Primary B cells from cord blood	blood
11	chr16:31313200-31313600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:31313200-31313600	Enhancers	GM12878-XiMat	blood

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