Variant report

Variant	rs233617
Chromosome Location	chr21:28397111-28397112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABPA-20	chr21:28396740-28397770	NONHSAT081556
2	lnc-GABPA-20	chr21:28396740-28397430	NONHSAT081558

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs233581	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs233582	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs233607	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs233609	0.81[EUR][1000 genomes]
rs233611	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs233612	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs233613	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs233618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs233619	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs233620	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2849664	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs394909	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs413156	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs427577	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs447687	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs545278	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs572317	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs636516	0.88[AMR][1000 genomes]
rs652277	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9978689	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2758532	chr21:28380230-28540443	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv2758817	chr21:28380230-28540443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv1066128	chr21:28382038-28403842	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	nsv1066134	chr21:28382038-28406482	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv1055852	chr21:28382038-28407515	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	nsv587341	chr21:28391743-28419053	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28351800-28416600	Weak transcription	Ovary	ovary
2	chr21:28391600-28400600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:28393200-28397600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:28395000-28397800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr21:28395400-28397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:28395800-28397200	Weak transcription	HSMMtube	muscle
7	chr21:28396000-28399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:28396400-28397200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr21:28396400-28397400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:28396400-28397600	Enhancers	NHDF-Ad	bronchial
11	chr21:28396400-28397800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr21:28396400-28398000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr21:28396400-28398600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr21:28396600-28397600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr21:28396600-28397600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:28396600-28397800	Enhancers	Hela-S3	cervix
17	chr21:28396600-28398200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr21:28396600-28399600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr21:28396800-28398200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr21:28397000-28397400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr21:28397000-28397600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr21:28397000-28397600	Enhancers	HSMM	muscle
23	chr21:28397000-28398800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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