Variant report

Variant	rs486507
Chromosome Location	chr11:58696118-58696119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYATL2-1	chr11:58695790-58696162	ENSG00000255523.1

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11229690	0.87[ASN][1000 genomes]
rs11229707	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11603726	0.84[ASN][1000 genomes]
rs1788552	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1892866	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1938785	0.87[ASN][1000 genomes]
rs1938787	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1938788	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2005121	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2105736	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2156322	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474121	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs478587	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs478705	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs480196	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482751	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs483991	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs488446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489782	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs489846	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501703	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs510360	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs513677	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516803	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs530481	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs532318	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs533087	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs535218	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538472	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544687	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs546051	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs550864	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs563370	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs564335	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs574058	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs576790	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7120597	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription 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	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3502182	chr11:58668199-58731237	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3502181	chr11:58668236-58731215	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3478019	chr11:58668282-58731214	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3478030	chr11:58668282-58731214	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3502183	chr11:58668353-58731177	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58694400-58696200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:58694800-58696200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:58694800-58696200	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:58694800-58696200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:58694800-58696200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:58694800-58696200	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr11:58694800-58696400	Flanking Active TSS	Fetal Intestine Large	intestine
8	chr11:58695000-58696200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:58695000-58696200	Flanking Active TSS	Liver	Liver
10	chr11:58695200-58696200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr11:58695200-58696200	Enhancers	Gastric	stomach
12	chr11:58695400-58696200	Active TSS	Fetal Kidney	kidney
13	chr11:58695400-58696200	Enhancers	Psoas Muscle	Psoas
14	chr11:58695400-58696400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr11:58695600-58696200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr11:58695600-58696200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr11:58695600-58696200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:58695600-58696200	Bivalent Enhancer	HepG2	liver
19	chr11:58695600-58696400	Enhancers	Stomach Mucosa	stomach
20	chr11:58695800-58696200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr11:58695800-58696200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:58695800-58696200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:58695800-58696200	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr11:58695800-58696200	Enhancers	Fetal Thymus	thymus
25	chr11:58695800-58696200	Enhancers	Thymus	Thymus
26	chr11:58695800-58696400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:58696000-58696200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr11:58696000-58696200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:58696000-58696200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:58696000-58696200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:58696000-58696200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr11:58696000-58696200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr11:58696000-58696200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr11:58696000-58696200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:58696000-58696200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:58696000-58696200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:58696000-58696200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:58696000-58696200	Enhancers	Fetal Muscle Leg	muscle
39	chr11:58696000-58696200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr11:58696000-58696200	Bivalent Enhancer	Small Intestine	intestine
41	chr11:58696000-58697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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