Variant report

Variant	rs875620
Chromosome Location	chr21:46682886-46682887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46677076..46679332-chr21:46681439..46683653,2	MCF-7	breast:
2	chr21:46675525..46679390-chr21:46682642..46685767,4	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1006779	0.83[AFR][1000 genomes]
rs1056099	0.88[ASN][1000 genomes]
rs1056100	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1056101	0.87[ASN][1000 genomes]
rs11558445	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11909411	0.86[ASN][1000 genomes]
rs13052344	0.85[ASN][1000 genomes]
rs2236443	0.88[ASN][1000 genomes]
rs2236444	0.88[ASN][1000 genomes]
rs2236445	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2236446	0.88[ASN][1000 genomes]
rs2236450	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246697	0.85[ASN][1000 genomes]
rs2255761	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255766	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2255774	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2256000	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297283	0.84[EUR][1000 genomes]
rs2330102	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2330103	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838852	0.83[ASN][1000 genomes]
rs2838854	0.89[ASN][1000 genomes]
rs2838855	0.89[ASN][1000 genomes]
rs2838857	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2838858	0.89[ASN][1000 genomes]
rs2838859	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838860	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838861	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838862	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28442024	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28501512	0.86[ASN][1000 genomes]
rs28576202	0.81[ASN][1000 genomes]
rs28616694	0.82[ASN][1000 genomes]
rs28622522	0.86[ASN][1000 genomes]
rs28623526	0.85[EUR][1000 genomes]
rs28676615	0.85[ASN][1000 genomes]
rs34956478	0.85[ASN][1000 genomes]
rs35776291	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35871601	0.82[ASN][1000 genomes]
rs3673	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4819050	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4819051	0.85[ASN][1000 genomes]
rs4819053	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7275382	0.85[ASN][1000 genomes]
rs7276591	0.86[ASN][1000 genomes]
rs7276828	0.88[ASN][1000 genomes]
rs7279136	0.88[ASN][1000 genomes]
rs7281263	0.85[ASN][1000 genomes]
rs8127834	0.82[ASN][1000 genomes]
rs8128636	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8132135	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8134011	0.90[ASN][1000 genomes]
rs8134084	0.85[ASN][1000 genomes]
rs875621	0.90[ASN][1000 genomes]
rs914214	0.84[ASN][1000 genomes]
rs914215	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs914218	0.85[ASN][1000 genomes]
rs9974891	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9977686	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9979545	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking 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 miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv914000	chr21:46647078-46765251	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
19	nsv914001	chr21:46647078-46944113	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
20	nsv914002	chr21:46655638-46945024	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
21	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
22	nsv914003	chr21:46670874-46695039	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv914004	chr21:46670874-46736694	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	nsv914005	chr21:46670874-46756700	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
25	nsv914006	chr21:46670874-46788299	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
26	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs875620	C21orf86	N/A	lymphoblastoid	RTeQTL
rs875620	LOC642852	Cis_1M	lymphoblastoid	RTeQTL
rs875620	C21orf86	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46669000-46683400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr21:46669200-46706600	Weak transcription	Right Atrium	heart
3	chr21:46671200-46683000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr21:46673800-46683400	Weak transcription	HSMM	muscle
5	chr21:46675600-46686200	Weak transcription	GM12878-XiMat	blood
6	chr21:46676000-46706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr21:46677000-46683400	Weak transcription	Primary T cells from cord blood	blood
8	chr21:46677000-46683800	Weak transcription	Primary B cells from cord blood	blood
9	chr21:46677200-46683200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr21:46677200-46683200	Weak transcription	Left Ventricle	heart
11	chr21:46677400-46683200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr21:46677400-46683200	Weak transcription	Right Ventricle	heart
13	chr21:46677400-46683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:46677400-46683600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr21:46677600-46683200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr21:46677600-46683200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr21:46677600-46683400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr21:46677600-46683400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr21:46677600-46683400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr21:46677600-46685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr21:46678000-46683200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr21:46678000-46683400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:46678000-46683400	Weak transcription	Fetal Thymus	thymus
24	chr21:46678000-46683600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr21:46678200-46683200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:46678600-46683000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr21:46678600-46683000	Weak transcription	Adipose Nuclei	Adipose
28	chr21:46678600-46683400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr21:46678600-46683600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr21:46678800-46683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr21:46678800-46684000	Weak transcription	Fetal Lung	lung
32	chr21:46678800-46689800	Weak transcription	A549	lung
33	chr21:46679000-46683400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr21:46679200-46683000	Weak transcription	Aorta	Aorta
35	chr21:46679400-46683400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr21:46679400-46683400	Weak transcription	Colonic Mucosa	Colon
37	chr21:46679600-46683400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr21:46679600-46683400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr21:46679600-46683400	Weak transcription	Brain Substantia Nigra	brain
40	chr21:46679800-46683200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr21:46679800-46683600	Weak transcription	NH-A	brain
42	chr21:46679800-46687200	Weak transcription	Fetal Heart	heart
43	chr21:46680000-46683200	Weak transcription	NHLF	lung
44	chr21:46680000-46689600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr21:46680200-46683000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr21:46680200-46683000	Weak transcription	Brain Anterior Caudate	brain
47	chr21:46680200-46683200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr21:46680200-46683400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr21:46680200-46683400	Weak transcription	Brain Angular Gyrus	brain
50	chr21:46680400-46683200	Weak transcription	Monocytes-CD14+_RO01746	blood

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