Variant report

Variant	rs2732540
Chromosome Location	chr11:35095486-35095487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APIP-1	chr11:35095464-35095505	XLOC_009415

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1116470	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1116471	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1425805	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1834459	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834460	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1895821	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2098878	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2553772	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2553773	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2553777	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2553783	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2553826	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2553827	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2732544	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732546	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2732547	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2732549	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2732550	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2732552	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2785152	0.82[EUR][1000 genomes]
rs2785193	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2785194	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2785197	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2785198	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2785201	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2785202	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs353590	0.81[JPT][hapmap]
rs353604	0.81[JPT][hapmap]
rs387619	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429503	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627096	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs675970	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693163	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs879487	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1826391	chr11:35000983-35098193	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv541000	chr11:35053717-35185471	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv541001	chr11:35053717-35224624	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv2757437	chr11:35067482-35238578	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv2752912	chr11:35074167-35238578	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv508623	chr11:35094933-35203363	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35088600-35099000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:35088800-35099200	Weak transcription	Stomach Mucosa	stomach
3	chr11:35089200-35098000	Weak transcription	Small Intestine	intestine
4	chr11:35091000-35098000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:35091200-35097600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr11:35091200-35099800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:35092200-35099000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:35093200-35095800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr11:35093400-35095600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr11:35094200-35095600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:35094200-35096400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:35094200-35097600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr11:35094200-35097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:35094400-35097600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:35094400-35097600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:35094600-35095800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:35094600-35095800	Enhancers	Osteobl	bone
18	chr11:35094800-35095800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr11:35094800-35096800	Weak transcription	Primary T cells from cord blood	blood
20	chr11:35094800-35098200	Weak transcription	Thymus	Thymus
21	chr11:35095000-35095600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:35095000-35095800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:35095000-35095800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:35095200-35096400	ZNF genes & repeats	GM12878-XiMat	blood
25	chr11:35095400-35095800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:35095400-35095800	Enhancers	K562	blood
27	chr11:35095400-35095800	Enhancers	NHDF-Ad	bronchial
28	chr11:35095400-35095800	Enhancers	NHEK	skin
29	chr11:35095400-35096000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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