Variant report

Variant	rs4819239
Chromosome Location	chr21:47760399-47760400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47740459..47742082-chr21:47759676..47761284,2	K562	blood:
2	chr21:47743944..47745871-chr21:47758860..47760421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160299	Chromatin interaction
ENSG00000160298	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10222102	0.83[EUR][1000 genomes]
rs10854482	0.80[YRI][hapmap]
rs11701361	1.00[YRI][hapmap]
rs13048286	0.81[ASN][1000 genomes]
rs13049522	0.84[CEU][hapmap]
rs17371795	0.94[CEU][hapmap]
rs1974172	0.81[ASN][1000 genomes]
rs2073378	0.84[JPT][hapmap]
rs2249060	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276258	0.92[AFR][1000 genomes]
rs2839222	0.83[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs2839223	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2839224	0.94[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes]
rs2839228	0.88[EUR][1000 genomes]
rs2839232	0.83[JPT][hapmap]
rs2839234	0.85[EUR][1000 genomes]
rs2839235	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2839251	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs28716675	0.82[EUR][1000 genomes]
rs34950974	0.80[EUR][1000 genomes]
rs35210219	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35274838	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35370178	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35449415	0.80[EUR][1000 genomes]
rs3788258	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3788261	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4818837	0.90[YRI][hapmap]
rs4819236	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4819241	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6518289	0.89[EUR][1000 genomes]
rs71326324	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7279052	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs7279193	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8131546	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9306152	0.94[CEU][hapmap];0.89[JPT][hapmap]
rs9637222	0.81[JPT][hapmap]
rs9979185	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9981892	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9983528	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9984689	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
32	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
33	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4819239	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs4819239	YBEY	cis	Heart Left Ventricle	GTEx
rs4819239	PCNT	cis	multi-tissue	Pritchard
rs4819239	YBEY	cis	Thyroid	GTEx
rs4819239	YBEY	cis	lung	GTEx
rs4819239	YBEY	cis	Whole Blood	GTEx
rs4819239	YBEY	cis	Adipose Subcutaneous	GTEx
rs4819239	YBEY	cis	Artery Tibial	GTEx
rs4819239	YBEY	cis	Esophagus Mucosa	GTEx
rs4819239	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs4819239	YBEY	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47745800-47762800	Weak transcription	Psoas Muscle	Psoas
2	chr21:47745800-47766400	Weak transcription	Small Intestine	intestine
3	chr21:47746000-47766400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr21:47746000-47793000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:47746200-47765600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr21:47746200-47769000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:47746400-47762400	Strong transcription	Fetal Stomach	stomach
8	chr21:47746400-47763400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:47746400-47766200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:47746400-47770200	Weak transcription	Fetal Brain Male	brain
11	chr21:47746400-47789200	Strong transcription	Fetal Muscle Leg	muscle
12	chr21:47746400-47792000	Weak transcription	Fetal Heart	heart
13	chr21:47746400-47797200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:47746600-47760400	Strong transcription	Fetal Brain Female	brain
15	chr21:47746600-47767600	Weak transcription	Right Atrium	heart
16	chr21:47747400-47760400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr21:47747600-47761400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr21:47747600-47787600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr21:47750000-47769000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr21:47751000-47765400	Weak transcription	Fetal Kidney	kidney
21	chr21:47751000-47766000	Weak transcription	Colon Smooth Muscle	Colon
22	chr21:47751800-47760400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr21:47753600-47760400	Strong transcription	Brain Hippocampus Middle	brain
24	chr21:47754000-47760400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr21:47754000-47760400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr21:47754000-47760400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:47754000-47760400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr21:47754000-47760400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr21:47754000-47761800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr21:47754000-47768000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr21:47754000-47778400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr21:47754000-47781400	Strong transcription	Thymus	Thymus
33	chr21:47754000-47787400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr21:47754000-47787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr21:47754200-47760400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr21:47754200-47760400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr21:47754200-47760400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr21:47754200-47760400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr21:47754200-47760400	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr21:47754200-47760400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr21:47754200-47760400	Strong transcription	Brain Germinal Matrix	brain
42	chr21:47754200-47760400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr21:47754200-47760400	Strong transcription	Placenta	Placenta
44	chr21:47754200-47760400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr21:47754200-47760400	Strong transcription	Spleen	Spleen
46	chr21:47754200-47760600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr21:47754200-47760800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr21:47754200-47761200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr21:47754200-47761400	Strong transcription	Liver	Liver
50	chr21:47754200-47762800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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