Variant report

Variant	rs10854480
Chromosome Location	chr21:47617810-47617811
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47614413..47616404-chr21:47616711..47619488,2	K562	blood:
2	chr21:47609281..47613722-chr21:47615252..47618849,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160285	Chromatin interaction
ENSG00000235878	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13046451	0.88[ASN][1000 genomes]
rs13049175	0.88[ASN][1000 genomes]
rs13052806	0.86[ASN][1000 genomes]
rs2001809	0.80[ASN][1000 genomes]
rs2187118	0.92[ASN][1000 genomes]
rs2187120	0.92[ASN][1000 genomes]
rs2187121	0.92[ASN][1000 genomes]
rs2187122	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2254524	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2277826	0.88[ASN][1000 genomes]
rs2280955	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280956	0.88[ASN][1000 genomes]
rs2280957	0.88[ASN][1000 genomes]
rs2280958	0.88[ASN][1000 genomes]
rs2280959	0.88[ASN][1000 genomes]
rs2330408	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839139	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839140	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2839141	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839144	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839145	0.84[ASN][1000 genomes]
rs2839146	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2839155	0.88[ASN][1000 genomes]
rs2839157	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2839161	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2968	0.89[ASN][1000 genomes]
rs35679325	0.88[ASN][1000 genomes]
rs4818828	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4819213	0.95[ASN][1000 genomes]
rs4819214	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819215	0.93[ASN][1000 genomes]
rs4819217	0.87[ASN][1000 genomes]
rs4819218	0.85[ASN][1000 genomes]
rs55689527	0.95[ASN][1000 genomes]
rs62212862	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518278	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6518282	0.85[ASN][1000 genomes]
rs6518285	0.86[ASN][1000 genomes]
rs7280110	0.95[ASN][1000 genomes]
rs7282841	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914247	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9717	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9976233	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9979525	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9984242	0.86[ASN][1000 genomes]
rs9984986	0.86[ASN][1000 genomes]
rs999691	0.89[EUR][1000 genomes];0.82[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	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
17	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
18	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
19	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
20	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
21	nsv914132	chr21:47572244-47619784	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
22	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
23	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
24	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
25	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
26	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
27	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10854480	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx
rs10854480	MCM3AP-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10854480	C21orf56	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr21:47605800-47621000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr21:47606600-47639800	Strong transcription	Fetal Brain Female	brain
8	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
10	chr21:47607800-47621000	Strong transcription	Liver	Liver
11	chr21:47608400-47621000	Strong transcription	Dnd41	blood
12	chr21:47608400-47622800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr21:47609000-47634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr21:47609200-47621000	Strong transcription	Fetal Muscle Leg	muscle
15	chr21:47609400-47618200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:47609400-47618200	Strong transcription	Colonic Mucosa	Colon
17	chr21:47609400-47621400	Weak transcription	A549	lung
18	chr21:47609400-47621600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr21:47609600-47623000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr21:47609800-47620000	Strong transcription	Lung	lung
21	chr21:47609800-47621000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr21:47609800-47621000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr21:47610000-47618200	Strong transcription	Fetal Intestine Small	intestine
24	chr21:47610000-47637600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr21:47610000-47644000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr21:47610200-47618200	Strong transcription	Brain Hippocampus Middle	brain
27	chr21:47610200-47618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr21:47610200-47621000	Strong transcription	Primary T cells from cord blood	blood
29	chr21:47610800-47621000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr21:47611000-47633600	Weak transcription	Right Atrium	heart
31	chr21:47611200-47622000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr21:47611600-47619400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr21:47611600-47619600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr21:47611600-47620400	Strong transcription	Left Ventricle	heart
35	chr21:47611600-47621000	Strong transcription	Brain Substantia Nigra	brain
36	chr21:47611600-47621800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr21:47611600-47623000	Strong transcription	Adipose Nuclei	Adipose
38	chr21:47611600-47642400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:47611600-47643400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr21:47611800-47618400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr21:47611800-47620800	Strong transcription	K562	blood
42	chr21:47611800-47621000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr21:47611800-47621000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr21:47611800-47621000	Strong transcription	HepG2	liver
45	chr21:47611800-47633400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr21:47611800-47634800	Strong transcription	NHDF-Ad	bronchial
47	chr21:47612000-47620600	Strong transcription	Brain Anterior Caudate	brain
48	chr21:47612000-47621000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:47612000-47621000	Strong transcription	HMEC	breast
50	chr21:47612000-47624200	Weak transcription	Small Intestine	intestine

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