Variant report

Variant	rs13052806
Chromosome Location	chr21:47645670-47645671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr21:47645590-47645788	HepG2	liver:	n/a	chr21:47645685-47645696
2	USF1	chr21:47645597-47645782	HepG2	liver:	n/a	chr21:47645685-47645696
3	FOSL2	chr21:47645596-47645852	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47645527..47650637-chr21:47703398..47707562,6	MCF-7	breast:
2	chr21:47639961..47644801-chr21:47645631..47650469,7	K562	blood:
3	chr21:47644824..47646810-chr21:47647997..47652112,4	K562	blood:
4	chr21:47645020..47650682-chr21:47742361..47746485,6	MCF-7	breast:
5	chr21:47639839..47642625-chr21:47644945..47648967,4	K562	blood:
6	chr21:47644893..47647018-chr21:47742616..47745455,2	K562	blood:

Variant related genes	Relation type
MCM3AP-AS1	TF binding region
ENSG00000160285	Chromatin interaction
ENSG00000182362	Chromatin interaction
ENSG00000215424	Chromatin interaction
ENSG00000223901	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000160299	Chromatin interaction
ENSG00000160298	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10854480	0.86[ASN][1000 genomes]
rs12482209	0.92[ASN][1000 genomes]
rs13046451	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13046494	0.87[ASN][1000 genomes]
rs13049175	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13049797	0.87[ASN][1000 genomes]
rs13049893	0.84[ASN][1000 genomes]
rs13050025	0.87[ASN][1000 genomes]
rs13051845	0.81[ASN][1000 genomes]
rs13052226	0.86[ASN][1000 genomes]
rs13052376	0.87[ASN][1000 genomes]
rs13052495	0.87[ASN][1000 genomes]
rs13052701	0.91[ASN][1000 genomes]
rs17176110	0.86[ASN][1000 genomes]
rs17176513	0.82[ASN][1000 genomes]
rs17176520	0.82[ASN][1000 genomes]
rs17183123	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2001289	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2001809	0.83[ASN][1000 genomes]
rs2014276	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2032226	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2156117	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187118	0.88[ASN][1000 genomes]
rs2187120	0.88[ASN][1000 genomes]
rs2187121	0.88[ASN][1000 genomes]
rs2187122	0.85[ASN][1000 genomes]
rs2250213	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2254524	0.87[ASN][1000 genomes]
rs2276257	0.86[ASN][1000 genomes]
rs2277826	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2280955	0.96[ASN][1000 genomes]
rs2280956	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280957	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280958	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280959	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2330353	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2330408	0.87[ASN][1000 genomes]
rs2839139	0.87[ASN][1000 genomes]
rs2839140	0.89[ASN][1000 genomes]
rs2839141	0.88[ASN][1000 genomes]
rs2839144	0.89[ASN][1000 genomes]
rs2839146	0.88[ASN][1000 genomes]
rs2839155	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2839157	0.96[ASN][1000 genomes]
rs2839160	0.93[ASN][1000 genomes]
rs2839161	0.93[ASN][1000 genomes]
rs2839167	0.92[ASN][1000 genomes]
rs2839170	0.88[ASN][1000 genomes]
rs2839171	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839173	0.86[ASN][1000 genomes]
rs2839174	0.86[ASN][1000 genomes]
rs2839175	0.88[ASN][1000 genomes]
rs2839176	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839196	0.89[ASN][1000 genomes]
rs2839197	0.87[ASN][1000 genomes]
rs2839199	0.85[ASN][1000 genomes]
rs2839200	0.87[ASN][1000 genomes]
rs2839984	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968	0.85[ASN][1000 genomes]
rs34586434	0.82[ASN][1000 genomes]
rs35679325	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3788252	0.88[ASN][1000 genomes]
rs4535149	0.85[ASN][1000 genomes]
rs4818828	0.87[ASN][1000 genomes]
rs4818832	0.87[ASN][1000 genomes]
rs4819213	0.89[ASN][1000 genomes]
rs4819214	0.88[ASN][1000 genomes]
rs4819215	0.88[ASN][1000 genomes]
rs4819217	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4819218	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819222	0.82[ASN][1000 genomes]
rs4819223	0.85[ASN][1000 genomes]
rs4819225	0.85[ASN][1000 genomes]
rs4819226	0.81[ASN][1000 genomes]
rs55689527	0.89[ASN][1000 genomes]
rs56840278	0.87[ASN][1000 genomes]
rs56955294	0.87[ASN][1000 genomes]
rs59828751	0.87[ASN][1000 genomes]
rs62212862	0.84[ASN][1000 genomes]
rs62226484	0.83[ASN][1000 genomes]
rs62226486	0.85[ASN][1000 genomes]
rs62226489	0.86[ASN][1000 genomes]
rs6518278	0.96[ASN][1000 genomes]
rs6518282	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6518285	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280110	0.89[ASN][1000 genomes]
rs7282841	0.88[ASN][1000 genomes]
rs8128380	0.90[ASN][1000 genomes]
rs914247	0.87[ASN][1000 genomes]
rs915803	0.82[ASN][1000 genomes]
rs915804	0.93[ASN][1000 genomes]
rs9717	0.85[ASN][1000 genomes]
rs9976233	0.89[ASN][1000 genomes]
rs9979525	0.88[ASN][1000 genomes]
rs9984242	0.98[ASN][1000 genomes]
rs9984708	0.93[ASN][1000 genomes]
rs9984986	0.95[ASN][1000 genomes]
rs999691	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13052806	YBEY	cis	Artery Tibial	GTEx
rs13052806	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx
rs13052806	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs13052806	YBEY	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
2	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
5	chr21:47614200-47646000	Weak transcription	Fetal Brain Male	brain
6	chr21:47614200-47646200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:47626000-47646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr21:47626400-47646400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr21:47627800-47647000	Weak transcription	Primary B cells from cord blood	blood
10	chr21:47629200-47646200	Weak transcription	Small Intestine	intestine
11	chr21:47630400-47647000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr21:47632800-47646000	Weak transcription	NH-A	brain
13	chr21:47638000-47645800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:47640600-47646200	Weak transcription	Fetal Lung	lung
15	chr21:47640800-47646000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr21:47641000-47647000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr21:47641600-47646000	Weak transcription	Colon Smooth Muscle	Colon
18	chr21:47641600-47646600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr21:47642200-47646000	Weak transcription	HSMMtube	muscle
20	chr21:47642600-47646000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:47642600-47646200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:47642600-47647000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr21:47642600-47647000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr21:47642600-47647200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr21:47642800-47646000	Weak transcription	Aorta	Aorta
26	chr21:47642800-47646200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr21:47642800-47646200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr21:47642800-47646200	Weak transcription	Fetal Heart	heart
29	chr21:47642800-47646800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr21:47642800-47647000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr21:47642800-47647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:47643000-47645800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr21:47643000-47646200	Weak transcription	Colonic Mucosa	Colon
34	chr21:47643000-47646400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr21:47643000-47647000	Weak transcription	Thymus	Thymus
36	chr21:47643200-47646200	Weak transcription	Primary T cells from cord blood	blood
37	chr21:47643200-47646200	Weak transcription	Brain Germinal Matrix	brain
38	chr21:47643200-47646200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr21:47643200-47647000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr21:47643200-47647200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:47643400-47645800	Weak transcription	Esophagus	oesophagus
42	chr21:47643400-47646000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr21:47643400-47646000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:47643400-47646000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr21:47643400-47646000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr21:47643400-47646000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:47643400-47646000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr21:47643400-47646000	Weak transcription	Fetal Brain Female	brain
49	chr21:47643400-47646000	Weak transcription	Placenta	Placenta
50	chr21:47643400-47646000	Weak transcription	Gastric	stomach

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