Variant report

Variant	rs2838520
Chromosome Location	chr21:45615896-45615897
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45593299..45595142-chr21:45615478..45617030,2	MCF-7	breast:
2	chr21:45557116..45559735-chr21:45615528..45618206,3	MCF-7	breast:
3	chr21:45615502..45617869-chr21:45667459..45670293,2	K562	blood:
4	chr21:45586838..45589344-chr21:45614842..45616536,2	MCF-7	breast:
5	chr21:45610715..45617377-chr21:45717031..45721978,7	MCF-7	breast:
6	chr21:45568616..45570755-chr21:45615083..45617675,2	K562	blood:
7	chr21:45609075..45610927-chr21:45615037..45616803,2	K562	blood:
8	chr21:45615189..45618434-chr21:45625221..45628569,5	MCF-7	breast:
9	chr21:45614676..45619255-chr21:45657692..45665676,14	MCF-7	breast:
10	chr21:45595676..45596715-chr21:45615636..45617128,25	MCF-7	breast:
11	chr21:45595680..45596514-chr21:45615830..45617060,14	MCF-7	breast:
12	chr21:45612993..45620081-chr21:45620303..45625017,17	MCF-7	breast:
13	chr21:45567927..45569479-chr21:45614833..45617390,2	K562	blood:
14	chr21:45607137..45608941-chr21:45615370..45617109,2	K562	blood:
15	chr21:45595676..45596652-chr21:45615636..45617063,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267913	Chromatin interaction
ENSG00000232124	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11089118	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2070551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838517	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838519	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2838521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876932	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35405602	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3746958	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3804031	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804032	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4317019	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456788	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276302	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7282490	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs743478	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743479	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762421	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762422	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762423	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127691	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134436	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	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
15	esv3411301	chr21:45609579-45620771	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	esv3455479	chr21:45609616-45620726	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv3455480	chr21:45609633-45620722	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	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
19	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2838520	WRB	cis	cerebellum	SCAN
rs2838520	C21orf2	cis	cerebellum	SCAN
rs2838520	AGPAT3	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45610400-45616000	Weak transcription	Thymus	Thymus
2	chr21:45610800-45616600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr21:45610800-45617600	Enhancers	Placenta	Placenta
4	chr21:45611200-45616200	Weak transcription	Gastric	stomach
5	chr21:45612000-45616200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:45612200-45617200	Enhancers	Fetal Muscle Leg	muscle
7	chr21:45612400-45616400	Weak transcription	Esophagus	oesophagus
8	chr21:45612600-45616000	Enhancers	Fetal Muscle Trunk	muscle
9	chr21:45612600-45616400	Weak transcription	Right Ventricle	heart
10	chr21:45612800-45616000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:45612800-45616000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:45612800-45616000	Weak transcription	Left Ventricle	heart
13	chr21:45612800-45617400	Enhancers	Primary hematopoietic stem cells	blood
14	chr21:45613200-45617000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr21:45613600-45617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr21:45613600-45617400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr21:45613600-45617400	Enhancers	Primary B cells from peripheral blood	blood
18	chr21:45614000-45616000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr21:45614000-45617000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr21:45614000-45617200	Enhancers	GM12878-XiMat	blood
21	chr21:45614000-45617600	Enhancers	Primary B cells from cord blood	blood
22	chr21:45614200-45616000	Weak transcription	Fetal Intestine Small	intestine
23	chr21:45614200-45616200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:45614400-45617400	Weak transcription	Brain Angular Gyrus	brain
25	chr21:45614600-45616000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr21:45614600-45616000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr21:45614600-45616000	Weak transcription	Stomach Mucosa	stomach
28	chr21:45614600-45616400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:45614600-45616600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:45614800-45616000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr21:45614800-45616400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:45614800-45616400	Weak transcription	Right Atrium	heart
33	chr21:45614800-45622400	Weak transcription	Pancreas	Pancrea
34	chr21:45615000-45616000	Weak transcription	Lung	lung
35	chr21:45615000-45616000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr21:45615000-45617200	Weak transcription	Colonic Mucosa	Colon
37	chr21:45615000-45623200	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:45615400-45616400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr21:45615400-45616800	Weak transcription	Brain Anterior Caudate	brain
40	chr21:45615400-45622200	Weak transcription	Fetal Lung	lung
41	chr21:45615600-45616000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr21:45615600-45616000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr21:45615600-45616800	Enhancers	Primary T cells from cord blood	blood
44	chr21:45615600-45616800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr21:45615600-45616800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr21:45615600-45617000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr21:45615600-45617000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr21:45615600-45617000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr21:45615600-45617000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr21:45615600-45617200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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