Variant report

Variant	rs12285495
Chromosome Location	chr11:71548520-71548521
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DEFB108B-2	chr11:71548445-71548756	NONHSAT022717

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10792941	0.82[EUR][1000 genomes]
rs11235058	0.82[EUR][1000 genomes]
rs11235176	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11235192	0.82[EUR][1000 genomes]
rs11606044	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12285436	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420318	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1806569	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1945051	0.84[EUR][1000 genomes]
rs2005541	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35755503	0.83[EUR][1000 genomes]
rs36088573	0.80[EUR][1000 genomes]
rs3750916	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3935051	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4122048	0.84[EUR][1000 genomes]
rs4245458	0.81[ASN][1000 genomes]
rs4316538	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4945296	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945297	0.82[EUR][1000 genomes]
rs4945298	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945299	0.86[EUR][1000 genomes]
rs61889032	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61889033	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6592380	0.84[EUR][1000 genomes]
rs7102608	0.84[EUR][1000 genomes]
rs7104538	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7104541	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7113289	0.85[EUR][1000 genomes]
rs7113497	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7120658	0.81[ASN][1000 genomes]
rs7127709	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129249	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7129417	0.84[EUR][1000 genomes]
rs7129769	0.83[EUR][1000 genomes]
rs7927726	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932698	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7941039	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7944189	0.84[EUR][1000 genomes]
rs7947421	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	esv3527986	chr11:71298409-71620955	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv3527987	chr11:71298409-71620955	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2761682	chr11:71299175-71619923	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv897904	chr11:71316093-71615727	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv972041	chr11:71330518-71615123	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv3369013	chr11:71338874-71612242	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv2758276	chr11:71363639-71657576	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	esv2759836	chr11:71363639-71657576	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
11	nsv897905	chr11:71371354-71615727	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv1819073	chr11:71371742-71618164	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv897907	chr11:71386905-71549174	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	esv11723	chr11:71498860-71553549	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv1804003	chr11:71512115-71563035	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv2760190	chr11:71513455-71552665	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv11824	chr11:71515433-71603968	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv8837	chr11:71517340-71559915	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
19	esv1794199	chr11:71517609-71550455	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv1803631	chr11:71521288-71560091	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12285495	FAM86C1	cis	Muscle Skeletal	GTEx
rs12285495	CTD-2313N18.5	cis	Muscle Skeletal	GTEx
rs12285495	FAM86C1	cis	Artery Aorta	GTEx
rs12285495	FAM86C1	cis	Whole Blood	GTEx
rs12285495	ALG1L9P	cis	Muscle Skeletal	GTEx
rs12285495	FAM86C1	cis	Artery Tibial	GTEx
rs12285495	FAM86C1	cis	Skin Sun Exposed Lower leg	GTEx
rs12285495	FAM86C1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71542600-71553400	Weak transcription	Fetal Stomach	stomach
2	chr11:71547800-71549200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:71548400-71548600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:71548400-71549400	Enhancers	HUES6 Cell Line	embryonic stem cell

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