Variant report

Variant	rs6518350
Chromosome Location	chr21:45621817-45621818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45621565..45624005-chr21:45712576..45714212,3	MCF-7	breast:
2	chr21:45620857..45623394-chr21:45709649..45711804,3	MCF-7	breast:
3	chr21:45620341..45625358-chr21:45718389..45721509,5	MCF-7	breast:
4	chr21:45588739..45594310-chr21:45621185..45624296,6	MCF-7	breast:
5	chr21:45577492..45580364-chr21:45620942..45622616,2	K562	blood:
6	chr21:45619816..45631884-chr21:45656529..45663802,30	MCF-7	breast:
7	chr21:45621014..45624737-chr21:45625090..45629806,7	K562	blood:
8	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
9	chr21:45621411..45624934-chr21:45718058..45721352,4	MCF-7	breast:
10	chr21:45621786..45624650-chr21:45632661..45635247,3	MCF-7	breast:
11	chr21:45621014..45626357-chr21:45626432..45630019,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf33-2	chr21:45621173-45621840	XLOC_013967
2	lnc-ICOSLG-1	chr21:45621679-45621840	NONHSAT082494

No data

Variant related genes	Relation type
ENSG00000225331	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000160224	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000232010	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12483372	0.81[AMR][1000 genomes]
rs3746959	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55708341	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55736164	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55893906	0.82[AMR][1000 genomes]
rs55965762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56132007	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56178904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56299324	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58139755	0.90[AFR][1000 genomes]
rs58911644	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59380543	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62228209	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62228210	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62228216	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6518351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7282137	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active 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 miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription 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	64 gene(s)	inside rSNPs	diseases
11	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
12	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
13	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	esv3529214	chr21:45617222-45622747	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv3455399	chr21:45617324-45622622	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	esv994385	chr21:45617619-45623578	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv587730	chr21:45619367-45627976	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	esv1794351	chr21:45619474-45627976	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	esv1798512	chr21:45619474-45629565	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	esv1834007	chr21:45619474-45629565	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv587738	chr21:45620353-45628374	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6518350	C21orf33	cis	parietal	SCAN
rs6518350	BACE2	cis	parietal	SCAN
rs6518350		cis	Lymphoblastoid	GTEx
rs6518350	IGSF5	cis	parietal	SCAN
rs6518350	Hs.124623	cis	multi-tissue	Pritchard
rs6518350	KRTAP12-1	cis	cerebellum	SCAN
rs6518350	TRPM2	cis	parietal	SCAN
rs6518350	C21orf2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45614800-45622400	Weak transcription	Pancreas	Pancrea
2	chr21:45615000-45623200	Weak transcription	Brain Hippocampus Middle	brain
3	chr21:45615400-45622200	Weak transcription	Fetal Lung	lung
4	chr21:45616600-45622000	Weak transcription	Lung	lung
5	chr21:45616600-45622200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr21:45616600-45622200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr21:45616800-45622000	Weak transcription	Left Ventricle	heart
8	chr21:45616800-45622200	Weak transcription	Fetal Intestine Small	intestine
9	chr21:45616800-45622200	Weak transcription	Spleen	Spleen
10	chr21:45616800-45626600	Weak transcription	Thymus	Thymus
11	chr21:45617000-45622400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr21:45617000-45626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr21:45617200-45622200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr21:45617200-45622600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:45617200-45623200	Weak transcription	GM12878-XiMat	blood
16	chr21:45617200-45624000	Weak transcription	Gastric	stomach
17	chr21:45617200-45626200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr21:45617400-45622400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr21:45617400-45622400	Weak transcription	Right Atrium	heart
20	chr21:45617400-45622600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr21:45617400-45622600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr21:45617400-45622600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr21:45617400-45622600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr21:45617400-45624200	Weak transcription	Brain Substantia Nigra	brain
25	chr21:45617400-45624200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr21:45617400-45626000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr21:45617600-45622000	Weak transcription	Right Ventricle	heart
28	chr21:45617600-45622200	Weak transcription	Primary B cells from cord blood	blood
29	chr21:45617600-45622200	Weak transcription	K562	blood
30	chr21:45617600-45622400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr21:45618000-45622000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr21:45618000-45622000	Weak transcription	Fetal Muscle Leg	muscle
33	chr21:45619800-45623400	Weak transcription	Stomach Mucosa	stomach
34	chr21:45620000-45622000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:45620000-45623600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr21:45620200-45622000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr21:45620400-45622800	Weak transcription	Brain Anterior Caudate	brain
38	chr21:45621200-45622200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr21:45621400-45622200	Enhancers	Placenta	Placenta
40	chr21:45621600-45623000	Enhancers	Esophagus	oesophagus

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