Variant report

Variant	rs2839198
Chromosome Location	chr21:47708254-47708255
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47703549..47712907-chr21:47732716..47739888,14	MCF-7	breast:
2	chr21:47708141..47711504-chr21:47716399..47719423,3	K562	blood:
3	chr21:47706653..47708384-chr21:47767921..47770700,2	MCF-7	breast:
4	chr21:47698481..47701314-chr21:47707160..47708823,2	MCF-7	breast:
5	chr21:47702524..47712328-chr21:47732975..47746274,46	K562	blood:
6	chr21:47705068..47711362-chr21:47735611..47740059,7	MCF-7	breast:
7	chr21:47702151..47710134-chr21:47741079..47747645,22	MCF-7	breast:
8	chr21:47557351..47559795-chr21:47707646..47710303,2	K562	blood:
9	chr21:47700722..47725192-chr21:47732201..47746452,77	K562	blood:
10	chr21:47701944..47708797-chr21:47740125..47746082,20	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160298	Chromatin interaction
ENSG00000160299	Chromatin interaction
ENSG00000160282	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11089053	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11089056	0.81[JPT][hapmap]
rs11701725	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs12626184	0.82[JPT][hapmap]
rs13049522	0.82[JPT][hapmap]
rs1556336	0.82[JPT][hapmap]
rs1556337	0.82[JPT][hapmap]
rs1888539	0.82[JPT][hapmap]
rs2075906	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2156116	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254522	0.81[CHB][hapmap]
rs2277824	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2839153	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2839156	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2839162	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2839163	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2839172	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839177	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839178	0.81[CHB][hapmap]
rs2839182	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839202	0.82[JPT][hapmap]
rs2839203	0.82[JPT][hapmap]
rs2839207	0.82[JPT][hapmap]
rs3747007	0.81[JPT][hapmap]
rs4818829	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4818831	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818834	0.82[JPT][hapmap]
rs4818835	0.82[JPT][hapmap]
rs6518283	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6518286	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7282352	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs8131960	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8133857	0.88[ASN][1000 genomes]
rs914248	0.82[JPT][hapmap]
rs914249	0.82[JPT][hapmap]
rs9976868	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9982623	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:32 , 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	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
4	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
14	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
15	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
16	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
17	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
18	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
19	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
20	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
21	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
22	nsv587975	chr21:47661235-47830843	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
23	nsv432159	chr21:47673247-47854392	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
24	nsv527355	chr21:47678774-47863025	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
25	nsv914135	chr21:47681041-47762374	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
26	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
27	nsv1064588	chr21:47700051-47788823	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
28	nsv544496	chr21:47700051-47788823	Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
29	nsv914137	chr21:47700498-47862624	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
30	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
31	nsv587977	chr21:47704896-47713086	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
32	nsv914139	chr21:47706737-47786494	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2839198	YBEY	cis	Artery Aorta	GTEx
rs2839198	YBEY	cis	Esophagus Muscularis	GTEx
rs2839198	YBEY	cis	Artery Tibial	GTEx
rs2839198	YBEY	cis	Nerve Tibial	GTEx
rs2839198	YBEY	cis	lung	GTEx
rs2839198	YBEY	cis	Thyroid	GTEx
rs2839198	YBEY	cis	Stomach	GTEx
rs2839198	YBEY	cis	Muscle Skeletal	GTEx
rs2839198	AP001468.1	cis	Whole Blood	GTEx
rs2839198	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs2839198	YBEY	cis	Esophagus Mucosa	GTEx
rs2839198	YBEY	cis	Adipose Subcutaneous	GTEx
rs2839198	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs2839198	YBEY	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47706800-47709800	Weak transcription	Spleen	Spleen
2	chr21:47707000-47709600	Weak transcription	Right Ventricle	heart
3	chr21:47707000-47709800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:47707000-47709800	Weak transcription	Gastric	stomach
5	chr21:47707000-47709800	Weak transcription	Lung	lung
6	chr21:47707000-47711200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr21:47707000-47711400	Weak transcription	Esophagus	oesophagus
8	chr21:47707000-47711400	Weak transcription	Left Ventricle	heart
9	chr21:47707000-47711400	Weak transcription	Ovary	ovary
10	chr21:47707000-47711400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr21:47707000-47715200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr21:47707000-47717400	Weak transcription	Small Intestine	intestine
13	chr21:47707200-47709000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr21:47707200-47709200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:47707200-47709200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr21:47707200-47709600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:47707200-47709800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr21:47707200-47709800	Weak transcription	Fetal Kidney	kidney
19	chr21:47707200-47711000	Weak transcription	Primary T cells from cord blood	blood
20	chr21:47707200-47711200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr21:47707200-47711200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr21:47707200-47711200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr21:47707200-47711200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr21:47707200-47711200	Weak transcription	Fetal Thymus	thymus
25	chr21:47707200-47711200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr21:47707200-47711200	Weak transcription	K562	blood
27	chr21:47707200-47711400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:47707200-47711400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr21:47707200-47711400	Weak transcription	Aorta	Aorta
30	chr21:47707200-47711400	Weak transcription	Brain Angular Gyrus	brain
31	chr21:47707200-47711400	Weak transcription	Brain Substantia Nigra	brain
32	chr21:47707200-47711400	Weak transcription	Thymus	Thymus
33	chr21:47707200-47714800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr21:47707200-47715000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr21:47707200-47715800	Weak transcription	Right Atrium	heart
36	chr21:47707200-47717400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr21:47707400-47708800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr21:47707400-47709000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:47707400-47709000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr21:47707400-47709200	Weak transcription	Brain Hippocampus Middle	brain
41	chr21:47707400-47709600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr21:47707400-47709800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr21:47707400-47709800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr21:47707400-47709800	Weak transcription	Colon Smooth Muscle	Colon
45	chr21:47707400-47709800	Weak transcription	Pancreas	Pancrea
46	chr21:47707400-47709800	Enhancers	Dnd41	blood
47	chr21:47707400-47709800	Weak transcription	NH-A	brain
48	chr21:47707400-47710400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr21:47707400-47710800	Weak transcription	Primary B cells from cord blood	blood
50	chr21:47707400-47711000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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