Variant report

Variant	rs3788258
Chromosome Location	chr21:47789854-47789855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47713494..47715322-chr21:47788049..47790112,2	K562	blood:
2	chr21:47788835..47791511-chr21:47799288..47801354,2	K562	blood:
3	chr21:47787244..47789996-chr21:47820361..47822942,3	K562	blood:
4	chr21:47713822..47715879-chr21:47788612..47790511,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10222102	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047209	0.85[ASN][1000 genomes]
rs1543756	0.83[ASN][1000 genomes]
rs2073378	0.85[ASN][1000 genomes]
rs2249060	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28385599	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2839223	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2839226	0.90[ASN][1000 genomes]
rs2839227	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839228	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839232	0.97[ASN][1000 genomes]
rs2839234	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2839235	0.97[ASN][1000 genomes]
rs2839240	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28716675	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34950974	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35274838	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35370178	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35449415	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788263	0.90[ASN][1000 genomes]
rs3788264	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818837	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4818840	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4819239	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4819240	0.84[ASN][1000 genomes]
rs4819241	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4819242	0.86[ASN][1000 genomes]
rs4819244	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6518289	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518291	0.89[ASN][1000 genomes]
rs71326324	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7279052	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7279193	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7279204	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7279344	0.89[ASN][1000 genomes]
rs7281373	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7281777	0.87[ASN][1000 genomes]
rs8131546	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9306152	0.86[ASN][1000 genomes]
rs9637173	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9978397	0.96[ASN][1000 genomes]
rs9979185	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9980404	0.85[ASN][1000 genomes]
rs9981170	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9981892	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9981941	0.82[AMR][1000 genomes]
rs9983528	0.86[EUR][1000 genomes]
rs9984599	0.87[ASN][1000 genomes]
rs9984689	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	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
25	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
26	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
27	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
28	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
29	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
30	nsv914142	chr21:47772468-47866227	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
31	nsv1062683	chr21:47788763-47851236	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
32	esv3358214	chr21:47789724-47794322	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3788258	YBEY	cis	Adipose Subcutaneous	GTEx
rs3788258	YBEY	cis	Thyroid	GTEx
rs3788258	YBEY	cis	Muscle Skeletal	GTEx
rs3788258	YBEY	cis	Stomach	GTEx
rs3788258	YBEY	cis	Heart Left Ventricle	GTEx
rs3788258	YBEY	cis	Skin Sun Exposed Lower leg	GTEx
rs3788258	YBEY	cis	Whole Blood	GTEx
rs3788258	YBEY	cis	Artery Aorta	GTEx
rs3788258	YBEY	cis	Artery Tibial	GTEx
rs3788258	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs3788258	YBEY	cis	Esophagus Mucosa	GTEx
rs3788258	YBEY	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47746000-47793000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:47746400-47792000	Weak transcription	Fetal Heart	heart
3	chr21:47746400-47797200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:47763800-47792400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr21:47764000-47798000	Strong transcription	Fetal Stomach	stomach
6	chr21:47764200-47792400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr21:47764200-47793200	Strong transcription	Dnd41	blood
8	chr21:47764200-47800200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:47764400-47797000	Strong transcription	Fetal Intestine Small	intestine
10	chr21:47764600-47790400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:47765400-47798400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr21:47768400-47795600	Weak transcription	Right Atrium	heart
13	chr21:47774200-47801400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr21:47775600-47857600	Weak transcription	Stomach Mucosa	stomach
15	chr21:47780600-47791800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:47780600-47793800	Strong transcription	Fetal Brain Female	brain
17	chr21:47780800-47790000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr21:47780800-47790200	Strong transcription	HepG2	liver
19	chr21:47780800-47790800	Strong transcription	Lung	lung
20	chr21:47781000-47790000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr21:47781000-47790200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:47781000-47792400	Strong transcription	Adipose Nuclei	Adipose
23	chr21:47781000-47792800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr21:47781000-47793000	Strong transcription	Brain Germinal Matrix	brain
25	chr21:47781200-47790200	Strong transcription	Left Ventricle	heart
26	chr21:47781800-47791800	Weak transcription	Fetal Brain Male	brain
27	chr21:47782000-47791600	Strong transcription	Gastric	stomach
28	chr21:47782400-47791600	Weak transcription	Fetal Kidney	kidney
29	chr21:47782600-47790000	Strong transcription	NHLF	lung
30	chr21:47783400-47797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:47783600-47790000	Strong transcription	Pancreas	Pancrea
32	chr21:47783800-47797000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr21:47784000-47791600	Weak transcription	HSMM	muscle
34	chr21:47785200-47790000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr21:47786200-47790000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr21:47786200-47802800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr21:47786400-47791600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr21:47786800-47791800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr21:47787000-47791600	Weak transcription	Fetal Lung	lung
40	chr21:47787200-47791600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr21:47787200-47813200	Weak transcription	NH-A	brain
42	chr21:47787400-47817000	Weak transcription	Small Intestine	intestine
43	chr21:47787600-47790000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr21:47787600-47790600	Genic enhancers	Fetal Thymus	thymus
45	chr21:47787800-47790000	Enhancers	Primary T cells from cord blood	blood
46	chr21:47787800-47791400	Weak transcription	K562	blood
47	chr21:47787800-47791600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr21:47787800-47791600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr21:47787800-47791600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:47787800-47791600	Weak transcription	Brain Hippocampus Middle	brain

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