Variant report

Variant	rs62096046
Chromosome Location	chr18:12730817-12730818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1062235	0.89[ASN][1000 genomes]
rs1129214	0.89[ASN][1000 genomes]
rs12373207	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12373259	0.87[ASN][1000 genomes]
rs12455268	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12455295	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12457771	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12458097	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12458895	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12954079	0.89[ASN][1000 genomes]
rs12957555	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12957603	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12957810	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12960623	0.96[ASN][1000 genomes]
rs12960997	0.89[ASN][1000 genomes]
rs12962598	0.89[ASN][1000 genomes]
rs12963505	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12964507	0.88[ASN][1000 genomes]
rs12965733	0.84[ASN][1000 genomes]
rs12965990	0.89[ASN][1000 genomes]
rs12966246	0.83[ASN][1000 genomes]
rs12966367	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12966424	0.89[ASN][1000 genomes]
rs12968771	0.96[ASN][1000 genomes]
rs12969300	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12969446	0.89[ASN][1000 genomes]
rs12969938	0.89[ASN][1000 genomes]
rs12971256	0.84[ASN][1000 genomes]
rs1362709	0.90[ASN][1000 genomes]
rs1549011	0.89[ASN][1000 genomes]
rs1592642	0.84[ASN][1000 genomes]
rs1592643	0.84[ASN][1000 genomes]
rs17616402	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1971702	0.83[ASN][1000 genomes]
rs2011575	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011579	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2051262	0.88[ASN][1000 genomes]
rs2302768	0.90[ASN][1000 genomes]
rs28820339	0.84[ASN][1000 genomes]
rs28832066	0.89[ASN][1000 genomes]
rs34040888	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34120824	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34277169	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34472716	0.81[ASN][1000 genomes]
rs34537593	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34632667	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34690304	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34847769	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322088	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35506854	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35634465	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35699948	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35898717	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809919	0.88[ASN][1000 genomes]
rs3902981	0.81[ASN][1000 genomes]
rs4296322	0.88[ASN][1000 genomes]
rs45589535	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45596833	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633785	0.89[ASN][1000 genomes]
rs55870255	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62095975	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62096023	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62096048	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6505760	0.84[ASN][1000 genomes]
rs66808227	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7233175	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233694	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7507018	0.89[ASN][1000 genomes]
rs8083182	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086099	0.84[ASN][1000 genomes]
rs8086265	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8086846	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8097134	0.84[ASN][1000 genomes]
rs9303774	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303775	0.89[ASN][1000 genomes]
rs9303776	0.87[ASN][1000 genomes]
rs933600	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948319	0.90[ASN][1000 genomes]
rs963920	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945140	0.89[ASN][1000 genomes]
rs9945644	0.89[ASN][1000 genomes]
rs9945801	0.89[ASN][1000 genomes]
rs9948844	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9949293	0.89[ASN][1000 genomes]
rs9950365	0.89[ASN][1000 genomes]
rs9951576	0.89[ASN][1000 genomes]
rs9952000	0.89[ASN][1000 genomes]
rs9954112	0.89[ASN][1000 genomes]
rs9955985	0.89[ASN][1000 genomes]
rs9957880	0.88[ASN][1000 genomes]
rs9958100	0.90[ASN][1000 genomes]
rs9958412	0.89[ASN][1000 genomes]
rs9959039	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9959458	0.89[ASN][1000 genomes]
rs9959536	0.88[ASN][1000 genomes]
rs9960555	0.88[ASN][1000 genomes]
rs9961799	0.84[ASN][1000 genomes]
rs9962006	0.89[ASN][1000 genomes]
rs9963809	0.84[ASN][1000 genomes]
rs9964868	0.92[ASN][1000 genomes]
rs9966464	0.88[ASN][1000 genomes]
rs9966490	0.90[ASN][1000 genomes]
rs9966672	0.90[ASN][1000 genomes]
rs9967437	0.89[ASN][1000 genomes]
rs9967553	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
9	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv909405	chr18:12727224-12750499	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv909406	chr18:12727224-12761498	ZNF genes & repeats Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1062149	chr18:12728115-12783898	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62096046	RP11-861E21.2	cis	Muscle Skeletal	GTEx
rs62096046	SPIRE1	cis	Muscle Skeletal	GTEx
rs62096046	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12723000-12748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:12726200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:12726600-12735600	Weak transcription	Right Atrium	heart
4	chr18:12727000-12745800	Weak transcription	Thymus	Thymus
5	chr18:12727200-12731800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:12727200-12740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:12728200-12731200	Weak transcription	HSMM	muscle
8	chr18:12729800-12731200	Enhancers	Hela-S3	cervix
9	chr18:12730200-12731000	Enhancers	A549	lung
10	chr18:12730600-12731200	Active TSS	Placenta	Placenta
11	chr18:12730600-12731600	Active TSS	HepG2	liver

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