Variant report

Variant	rs9860091
Chromosome Location	chr3:99013781-99013782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10154853	0.82[ASN][1000 genomes]
rs10511173	0.96[ASN][1000 genomes]
rs10804726	0.88[ASN][1000 genomes]
rs10804727	0.88[ASN][1000 genomes]
rs10935708	0.88[ASN][1000 genomes]
rs1118911	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11721251	0.92[ASN][1000 genomes]
rs13061712	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13073431	0.88[ASN][1000 genomes]
rs1318850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356924	0.90[ASN][1000 genomes]
rs1383839	0.88[EUR][1000 genomes]
rs1402263	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1402266	0.94[ASN][1000 genomes]
rs1402267	0.92[ASN][1000 genomes]
rs1402268	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520669	0.81[ASN][1000 genomes]
rs1520670	0.81[ASN][1000 genomes]
rs1520678	0.92[ASN][1000 genomes]
rs1520692	0.90[ASN][1000 genomes]
rs1520693	0.90[ASN][1000 genomes]
rs1520694	0.90[ASN][1000 genomes]
rs1568426	0.88[ASN][1000 genomes]
rs1574857	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829553	0.90[ASN][1000 genomes]
rs1996654	0.90[ASN][1000 genomes]
rs2128024	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139702	0.92[ASN][1000 genomes]
rs2170387	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170388	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2200017	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341809	0.90[ASN][1000 genomes]
rs2341812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341813	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2880156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4312686	0.90[ASN][1000 genomes]
rs4327425	0.90[ASN][1000 genomes]
rs4426705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4572803	0.90[ASN][1000 genomes]
rs4572804	0.90[ASN][1000 genomes]
rs4629370	0.88[ASN][1000 genomes]
rs4928128	0.88[ASN][1000 genomes]
rs4928176	0.81[ASN][1000 genomes]
rs4928177	0.88[ASN][1000 genomes]
rs4928179	0.88[ASN][1000 genomes]
rs4928180	0.88[ASN][1000 genomes]
rs59089459	0.86[EUR][1000 genomes]
rs62283771	0.86[EUR][1000 genomes]
rs6440496	0.88[ASN][1000 genomes]
rs6440525	0.86[EUR][1000 genomes]
rs6776314	0.88[ASN][1000 genomes]
rs6784043	0.90[ASN][1000 genomes]
rs6786590	0.90[ASN][1000 genomes]
rs6800453	0.92[ASN][1000 genomes]
rs71620012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73138428	0.86[EUR][1000 genomes]
rs7373550	0.90[ASN][1000 genomes]
rs7374314	0.90[ASN][1000 genomes]
rs7614880	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620378	0.88[ASN][1000 genomes]
rs7628173	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7645284	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289771	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9289774	0.86[AMR][1000 genomes]
rs974686	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823613	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831801	0.97[ASN][1000 genomes]
rs9856699	0.88[ASN][1000 genomes]
rs9867001	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798220	chr3:98894142-99020463	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1002786	chr3:98944446-99013936	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv818163	chr3:99005053-99015616	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9860091	NAPEPLD	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99013000-99013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:99013000-99014000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:99013200-99013800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:99013200-99013800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:99013200-99014000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:99013200-99014200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:99013400-99013800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:99013400-99013800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:99013400-99014000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:99013400-99014000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:99013400-99014000	Enhancers	Fetal Kidney	kidney
12	chr3:99013400-99014000	Enhancers	Dnd41	blood
13	chr3:99013600-99013800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:99013600-99014000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:99013600-99014000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:99013600-99014200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:99013600-99014200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr3:99013600-99014400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:99013600-99014400	Enhancers	HUES64 Cell Line	embryonic stem cell

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