Variant report

Variant	rs8062324
Chromosome Location	chr16:79784974-79784975
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:79780045..79782681-chr16:79783424..79786926,3	K562	blood:
2	chr16:79782700..79785427-chr16:79803858..79806131,2	MCF-7	breast:
3	chr16:79762471..79764929-chr16:79784561..79786086,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAF-2	chr16:79784589-79785173	ENSG00000261390.1

Variant related genes	Relation type
ENSG00000260876	Chromatin interaction
ENSG00000261390	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10871378	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs11860057	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11861737	0.82[JPT][hapmap]
rs12448881	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12599770	0.88[JPT][hapmap]
rs12716880	0.85[EUR][1000 genomes]
rs13334268	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs13337701	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13337703	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13338008	0.87[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs13338235	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16951260	0.86[ASN][1000 genomes]
rs16951261	0.86[ASN][1000 genomes]
rs16951264	0.84[ASN][1000 genomes]
rs16951284	0.85[ASN][1000 genomes]
rs16951299	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs16951301	0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs16951302	0.85[ASN][1000 genomes]
rs16951303	0.85[ASN][1000 genomes]
rs16951310	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs16951312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16951318	0.85[ASN][1000 genomes]
rs16951320	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs16951359	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28420623	0.85[ASN][1000 genomes]
rs28433357	0.85[ASN][1000 genomes]
rs28536718	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28691811	0.85[ASN][1000 genomes]
rs4257219	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4296269	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4302049	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4319779	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319782	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4322684	0.85[ASN][1000 genomes]
rs4327063	0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs4372706	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4411509	0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4470160	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4485383	0.85[JPT][hapmap]
rs4528586	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4567730	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4567731	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4603571	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4614737	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4632145	0.82[ASN][1000 genomes]
rs4632146	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633733	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889024	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889026	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs56986701	0.82[ASN][1000 genomes]
rs59680118	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60153062	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62041321	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62041342	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62041343	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564696	0.83[ASN][1000 genomes]
rs6564697	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564698	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564699	0.85[ASN][1000 genomes]
rs6564700	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6564701	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6564702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6564703	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6564704	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67364537	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7187216	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7190102	0.92[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7190298	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7191995	0.86[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7199398	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7200600	0.83[ASN][1000 genomes]
rs7200937	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7205712	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72810418	0.84[ASN][1000 genomes]
rs72810426	0.84[ASN][1000 genomes]
rs72810440	0.82[ASN][1000 genomes]
rs8045678	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs8052982	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8053230	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8057083	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8060038	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs8060072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8061610	0.85[ASN][1000 genomes]
rs8063650	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9673780	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673947	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9921624	0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9922033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9923844	0.92[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9925997	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9926635	0.85[ASN][1000 genomes]
rs9927594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9927598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9928163	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9929497	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9931431	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936175	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9936192	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9936261	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9939090	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9939565	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8062324	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79772600-79785600	Weak transcription	Fetal Lung	lung
2	chr16:79782600-79785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:79783400-79785000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:79783600-79788400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr16:79783600-79789000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr16:79783800-79786600	Weak transcription	Fetal Thymus	thymus
7	chr16:79784000-79787200	Weak transcription	Lung	lung
8	chr16:79784200-79786800	Enhancers	Fetal Muscle Leg	muscle
9	chr16:79784400-79785000	Weak transcription	Fetal Intestine Small	intestine
10	chr16:79784400-79786000	Weak transcription	Colon Smooth Muscle	Colon
11	chr16:79784800-79785200	Weak transcription	Rectal Smooth Muscle	rectum

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