Variant report

Variant	rs845587
Chromosome Location	chr20:12744198-12744199
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTLC3-8	chr20:12743475-12745586	NONHSAT078657

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11087035	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1739566	0.80[EUR][1000 genomes]
rs708957	0.80[EUR][1000 genomes]
rs845565	0.82[EUR][1000 genomes]
rs845580	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs845581	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs864625	1.00[EUR][1000 genomes];1.00[ASN][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	esv18943	chr20:12627634-12841804	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv585433	chr20:12724326-12756660	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
3	nsv1066818	chr20:12729400-12781534	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
4	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1065145	chr20:12729803-12781534	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
6	nsv522376	chr20:12730872-12771339	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
7	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12741200-12758600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:12742200-12744200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr20:12742400-12744400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:12742600-12744200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
5	chr20:12742600-12744200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr20:12742800-12744200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:12743000-12745400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr20:12743400-12744200	Enhancers	Ovary	ovary
9	chr20:12743400-12744200	Enhancers	Rectal Smooth Muscle	rectum
10	chr20:12743400-12744400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr20:12743600-12744400	Enhancers	Fetal Heart	heart
12	chr20:12743600-12744400	Enhancers	Fetal Kidney	kidney
13	chr20:12743600-12744400	Enhancers	Lung	lung
14	chr20:12743800-12744200	Enhancers	Aorta	Aorta
15	chr20:12743800-12744200	Enhancers	Brain Angular Gyrus	brain
16	chr20:12743800-12744400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr20:12743800-12745000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr20:12743800-12745600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:12744000-12744200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr20:12744000-12744400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr20:12744000-12744400	Genic enhancers	H9 Cell Line	embryonic stem cell
22	chr20:12744000-12744400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr20:12744000-12745200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:12744000-12745400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:12744000-12745800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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