Variant report

Variant	rs55689527
Chromosome Location	chr21:47622727-47622728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47620347..47622870-chr21:47628360..47630979,2	K562	blood:
2	chr21:47621818..47625200-chr21:47640268..47643011,3	K562	blood:
3	chr21:47621595..47623797-chr21:47628982..47632480,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10854480	0.95[ASN][1000 genomes]
rs12482209	0.81[ASN][1000 genomes]
rs13046451	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13049175	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13052701	0.81[ASN][1000 genomes]
rs13052806	0.89[ASN][1000 genomes]
rs2001809	0.82[ASN][1000 genomes]
rs2187118	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187120	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187121	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187122	0.94[ASN][1000 genomes]
rs2254524	0.97[ASN][1000 genomes]
rs2277826	0.89[ASN][1000 genomes]
rs2280955	0.88[ASN][1000 genomes]
rs2280956	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280957	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280958	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280959	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2330408	0.96[ASN][1000 genomes]
rs2839139	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2839140	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839141	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2839144	0.98[ASN][1000 genomes]
rs2839145	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2839146	0.97[ASN][1000 genomes]
rs2839155	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839157	0.88[ASN][1000 genomes]
rs2839160	0.83[ASN][1000 genomes]
rs2839161	0.83[ASN][1000 genomes]
rs2839167	0.81[ASN][1000 genomes]
rs2968	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35679325	0.90[ASN][1000 genomes]
rs4818828	0.97[ASN][1000 genomes]
rs4819213	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819214	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4819215	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819217	0.88[ASN][1000 genomes]
rs4819218	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62212862	0.95[ASN][1000 genomes]
rs6518278	0.88[ASN][1000 genomes]
rs6518282	0.88[ASN][1000 genomes]
rs6518285	0.89[ASN][1000 genomes]
rs7280110	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282841	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs914247	0.96[ASN][1000 genomes]
rs915804	0.82[ASN][1000 genomes]
rs9717	0.94[ASN][1000 genomes]
rs9976233	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979525	0.99[ASN][1000 genomes]
rs9984242	0.88[ASN][1000 genomes]
rs9984708	0.83[ASN][1000 genomes]
rs9984986	0.89[ASN][1000 genomes]
rs999691	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1061087	chr21:47476088-47643219	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
17	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
18	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
19	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
20	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
21	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
22	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
23	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
24	nsv1062031	chr21:47608580-47643219	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
25	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
26	esv3354277	chr21:47619724-47624222	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
27	esv3350903	chr21:47621024-47623322	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs55689527	YBEY	cis	Esophagus Mucosa	GTEx
rs55689527	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs55689527	MCM3AP-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs55689527	YBEY	cis	Whole Blood	GTEx
rs55689527	YBEY	cis	Artery Tibial	GTEx
rs55689527	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47605000-47633200	Weak transcription	Stomach Mucosa	stomach
2	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
3	chr21:47605400-47625600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr21:47606600-47639800	Strong transcription	Fetal Brain Female	brain
7	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
9	chr21:47608400-47622800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr21:47609000-47634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr21:47609600-47623000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr21:47610000-47637600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:47610000-47644000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr21:47611000-47633600	Weak transcription	Right Atrium	heart
15	chr21:47611600-47623000	Strong transcription	Adipose Nuclei	Adipose
16	chr21:47611600-47642400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr21:47611600-47643400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:47611800-47633400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr21:47611800-47634800	Strong transcription	NHDF-Ad	bronchial
20	chr21:47612000-47624200	Weak transcription	Small Intestine	intestine
21	chr21:47612000-47635600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr21:47612200-47644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr21:47612200-47645600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr21:47612400-47644400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:47614200-47622800	Weak transcription	NH-A	brain
26	chr21:47614200-47646000	Weak transcription	Fetal Brain Male	brain
27	chr21:47614200-47646200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:47616000-47625000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr21:47616000-47625000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:47616200-47624800	Weak transcription	Hela-S3	cervix
31	chr21:47616200-47633200	Weak transcription	Fetal Heart	heart
32	chr21:47616400-47623600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr21:47616800-47622800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr21:47617000-47625000	Weak transcription	Right Ventricle	heart
35	chr21:47617000-47640400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr21:47618200-47625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr21:47618400-47624000	Strong transcription	NHLF	lung
38	chr21:47618400-47626200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr21:47618400-47643400	Strong transcription	NHEK	skin
40	chr21:47618800-47622800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr21:47618800-47623600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr21:47619200-47634600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr21:47619200-47643400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr21:47619400-47623200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:47619400-47625200	Strong transcription	HSMMtube	muscle
46	chr21:47619800-47622800	Weak transcription	Brain Angular Gyrus	brain
47	chr21:47619800-47623400	Weak transcription	Fetal Lung	lung
48	chr21:47619800-47625000	Weak transcription	Primary B cells from cord blood	blood
49	chr21:47620000-47622800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr21:47620000-47624200	Weak transcription	GM12878-XiMat	blood

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