Variant report

Variant	rs4497482
Chromosome Location	chr12:8609674-8609675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC4D-3	chr12:8609386-8610056	l_593_chr12:8608782-8610056_testes

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10734709	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10743393	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10743396	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770711	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770722	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10770723	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10770734	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770735	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770736	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770737	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770738	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770739	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770740	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10841595	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11045398	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11045427	0.94[EUR][1000 genomes]
rs11829089	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12300621	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12302015	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12370044	0.92[EUR][1000 genomes]
rs4242888	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4242889	0.83[AMR][1000 genomes]
rs4242892	0.81[AMR][1000 genomes]
rs4255605	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4264222	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4296104	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4326877	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4343097	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4387429	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4388969	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4402377	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4420348	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4420349	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4420350	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4435079	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4528410	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4565980	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4576903	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4616119	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4622339	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4623977	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4623978	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4625553	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4628756	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4638374	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4640002	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4641551	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4882942	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4883145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4883146	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4883147	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4883148	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4883149	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61920546	0.86[EUR][1000 genomes]
rs6487135	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487136	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7302950	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304092	0.93[EUR][1000 genomes]
rs7306661	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7312356	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7968198	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7969317	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7969325	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv427902	chr12:8276546-8623987	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1044543	chr12:8449100-8792569	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1039504	chr12:8494944-8780137	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv557342	chr12:8599397-8774527	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	10 gene(s)	inside rSNPs	diseases
10	nsv933050	chr12:8602789-8775989	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4497482	CLEC6A	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8602200-8615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:8604200-8609800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:8606000-8610600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:8606800-8610000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:8606800-8613400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:8607000-8610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:8607200-8610400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:8607600-8614000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:8608800-8613400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:8609000-8610400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:8609000-8613400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:8609000-8613400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:8609200-8610600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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