Variant report

Variant	rs28856972
Chromosome Location	chr21:47868468-47868469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47866837..47868602-chr21:47869569..47871352,2	K562	blood:
2	chr21:47866658..47869357-chr21:47870152..47873599,4	MCF-7	breast:
3	chr21:47866415..47869098-chr21:47869186..47871401,3	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10483082	1.00[ASN][1000 genomes]
rs11909415	1.00[ASN][1000 genomes]
rs11909799	0.82[EUR][1000 genomes]
rs11910341	1.00[ASN][1000 genomes]
rs11910459	1.00[ASN][1000 genomes]
rs11910912	1.00[ASN][1000 genomes]
rs11911797	1.00[ASN][1000 genomes]
rs12106325	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979185	0.87[EUR][1000 genomes]
rs16979206	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979207	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979333	1.00[ASN][1000 genomes]
rs2096506	1.00[ASN][1000 genomes]
rs2839213	1.00[ASN][1000 genomes]
rs2839214	1.00[ASN][1000 genomes]
rs2839216	1.00[ASN][1000 genomes]
rs2839221	1.00[ASN][1000 genomes]
rs2839263	0.84[AFR][1000 genomes]
rs2839307	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28583333	1.00[ASN][1000 genomes]
rs28802698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28803288	1.00[ASN][1000 genomes]
rs28888425	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35945564	1.00[ASN][1000 genomes]
rs55742016	0.87[EUR][1000 genomes]
rs56077060	1.00[ASN][1000 genomes]
rs57108405	0.87[EUR][1000 genomes]
rs57134378	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57227186	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57819744	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57936960	1.00[ASN][1000 genomes]
rs58228841	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58468580	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58572600	0.87[EUR][1000 genomes]
rs58960215	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59691259	1.00[ASN][1000 genomes]
rs60091558	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60446383	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60455426	1.00[ASN][1000 genomes]
rs61013937	1.00[ASN][1000 genomes]
rs61160919	1.00[ASN][1000 genomes]
rs61407822	1.00[ASN][1000 genomes]
rs61485237	1.00[ASN][1000 genomes]
rs61735543	0.82[EUR][1000 genomes]
rs61735812	0.82[EUR][1000 genomes]
rs6518290	1.00[ASN][1000 genomes]
rs7278766	1.00[ASN][1000 genomes]
rs7282858	1.00[ASN][1000 genomes]
rs73371913	1.00[ASN][1000 genomes]
rs73372056	1.00[ASN][1000 genomes]
rs73372067	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73373837	1.00[ASN][1000 genomes]
rs73373844	1.00[ASN][1000 genomes]
rs73373855	1.00[ASN][1000 genomes]
rs73373860	1.00[ASN][1000 genomes]
rs73373920	1.00[ASN][1000 genomes]
rs73379336	1.00[ASN][1000 genomes]
rs73379382	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73381173	0.82[EUR][1000 genomes]
rs73381193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73381196	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383320	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73383347	1.00[ASN][1000 genomes]
rs73907470	1.00[ASN][1000 genomes]
rs73907473	1.00[ASN][1000 genomes]
rs73907474	1.00[ASN][1000 genomes]
rs8129476	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132727	1.00[ASN][1000 genomes]
rs8133340	1.00[ASN][1000 genomes]
rs881923	1.00[ASN][1000 genomes]
rs9680343	1.00[ASN][1000 genomes]
rs9941876	1.00[ASN][1000 genomes]
rs9941895	1.00[ASN][1000 genomes]
rs9974760	1.00[ASN][1000 genomes]
rs9975723	1.00[ASN][1000 genomes]
rs9975751	1.00[ASN][1000 genomes]
rs9976401	1.00[ASN][1000 genomes]
rs9979271	1.00[ASN][1000 genomes]
rs9981125	1.00[ASN][1000 genomes]
rs9982112	1.00[ASN][1000 genomes]
rs9982810	1.00[ASN][1000 genomes]
rs9983644	1.00[ASN][1000 genomes]
rs9984735	1.00[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	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
4	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
5	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
6	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
7	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
12	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
13	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
14	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
15	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
16	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
17	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
18	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
19	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
20	nsv587995	chr21:47803949-47877594	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
21	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
22	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
25	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
26	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28856972	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47803200-47872400	Weak transcription	Fetal Kidney	kidney
2	chr21:47828600-47872400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr21:47836800-47872400	Weak transcription	Right Atrium	heart
4	chr21:47845600-47877400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr21:47851000-47876000	Weak transcription	Small Intestine	intestine
6	chr21:47857400-47868600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:47858400-47877400	Weak transcription	Stomach Mucosa	stomach
8	chr21:47861200-47874000	Weak transcription	NH-A	brain
9	chr21:47861400-47869600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr21:47862000-47874000	Weak transcription	Psoas Muscle	Psoas
11	chr21:47862000-47876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr21:47862200-47868800	Weak transcription	Primary B cells from cord blood	blood
13	chr21:47862400-47876200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr21:47862800-47869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr21:47863000-47877200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr21:47863200-47870800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr21:47863200-47874000	Weak transcription	Colon Smooth Muscle	Colon
18	chr21:47863200-47874000	Weak transcription	HUVEC	blood vessel
19	chr21:47863200-47874200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr21:47863200-47876600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr21:47863200-47877200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:47863400-47874000	Weak transcription	Brain Angular Gyrus	brain
23	chr21:47863400-47874000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr21:47863400-47874000	Weak transcription	Osteobl	bone
25	chr21:47863400-47874200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:47863400-47874600	Weak transcription	Adipose Nuclei	Adipose
27	chr21:47864000-47871400	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:47864000-47871400	Weak transcription	Ovary	ovary
29	chr21:47864000-47874200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:47864000-47875600	Weak transcription	Esophagus	oesophagus
31	chr21:47864200-47872200	Weak transcription	Fetal Heart	heart
32	chr21:47864200-47874600	Weak transcription	Lung	lung
33	chr21:47864400-47872600	Weak transcription	Pancreas	Pancrea
34	chr21:47864400-47874000	Weak transcription	Brain Anterior Caudate	brain
35	chr21:47864400-47874000	Weak transcription	Gastric	stomach
36	chr21:47864400-47875400	Weak transcription	NHLF	lung
37	chr21:47864600-47877800	Weak transcription	Aorta	Aorta
38	chr21:47864800-47875800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr21:47865000-47874200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr21:47865000-47874200	Weak transcription	HMEC	breast
41	chr21:47865400-47876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr21:47865600-47868600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr21:47865600-47869600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr21:47865600-47872000	Weak transcription	Brain Substantia Nigra	brain
45	chr21:47865600-47872000	Weak transcription	Left Ventricle	heart
46	chr21:47865600-47873800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr21:47865600-47874400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr21:47865600-47874600	Weak transcription	Liver	Liver
49	chr21:47865600-47875200	Weak transcription	NHDF-Ad	bronchial
50	chr21:47865800-47874200	Weak transcription	Hela-S3	cervix

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