Variant report

Variant	rs1986277
Chromosome Location	chr11:77282207-77282208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSF1-1	chr11:77282102-77282547	XLOC_009511

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12417215	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12418261	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12419186	0.96[AMR][1000 genomes]
rs12420021	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12421695	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12574660	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12575305	0.93[AMR][1000 genomes]
rs12575763	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1945751	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2156842	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2187547	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2276415	0.80[EUR][1000 genomes]
rs2276416	0.80[EUR][1000 genomes]
rs4301811	0.87[AMR][1000 genomes]
rs4399350	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4553396	0.91[AMR][1000 genomes]
rs4606503	0.93[AMR][1000 genomes]
rs4945182	0.94[AMR][1000 genomes]
rs4945183	0.85[AMR][1000 genomes]
rs56175172	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57588070	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59581090	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59983642	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60045757	0.85[AMR][1000 genomes]
rs60842160	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60849458	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6592736	0.82[AMR][1000 genomes]
rs67062156	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67843465	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs68052959	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7119934	0.85[AMR][1000 genomes]
rs72943487	0.84[AMR][1000 genomes]
rs72943494	0.87[AMR][1000 genomes]
rs72943497	0.87[AMR][1000 genomes]
rs72945524	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7932111	0.93[AMR][1000 genomes]
rs7932603	0.93[AMR][1000 genomes]
rs7933197	0.96[AMR][1000 genomes]
rs7947430	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7950612	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1986277	AAMDC	cis	Artery Tibial	GTEx
rs1986277	RP11-91P24.7	cis	Artery Tibial	GTEx
rs1986277	RP11-91P24.6	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77272400-77282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:77278400-77282600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:77278400-77283000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:77279200-77283800	Enhancers	Pancreas	Pancrea
5	chr11:77279600-77284800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:77280000-77282800	Enhancers	Fetal Stomach	stomach
7	chr11:77280400-77282400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:77280400-77282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:77280600-77282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:77280600-77282400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:77280600-77282600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:77280600-77283000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:77280800-77282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:77280800-77282800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:77280800-77299600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:77281000-77283000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:77281400-77282600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:77281600-77282400	Active TSS	Ovary	ovary
19	chr11:77281800-77282600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:77282000-77282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:77282000-77282400	Enhancers	Fetal Lung	lung

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