Variant report

Variant	rs2001809
Chromosome Location	chr21:47631199-47631200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47630285..47633645-chr21:47635626..47637637,3	MCF-7	breast:
2	chr21:47626052..47633626-chr21:47637983..47644537,9	K562	blood:
3	chr21:47626033..47631308-chr21:47647803..47651413,4	K562	blood:
4	chr21:47621595..47623797-chr21:47628982..47632480,3	MCF-7	breast:
5	chr21:47626261..47629993-chr21:47630409..47632980,5	K562	blood:
6	chr21:47613596..47616132-chr21:47629781..47631506,2	K562	blood:
7	chr21:47565843..47568762-chr21:47630878..47633801,2	K562	blood:

Variant related genes	Relation type
ENSG00000223901	Chromatin interaction
ENSG00000160282	Chromatin interaction
ENSG00000215424	Chromatin interaction
ENSG00000160285	Chromatin interaction
ENSG00000235878	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10854480	0.80[ASN][1000 genomes]
rs13046451	0.84[ASN][1000 genomes]
rs13049175	0.84[ASN][1000 genomes]
rs13052806	0.83[ASN][1000 genomes]
rs2254524	0.84[ASN][1000 genomes]
rs2277826	0.84[ASN][1000 genomes]
rs2280955	0.87[ASN][1000 genomes]
rs2280956	0.84[ASN][1000 genomes]
rs2280957	0.84[ASN][1000 genomes]
rs2280958	0.84[ASN][1000 genomes]
rs2280959	0.84[ASN][1000 genomes]
rs2839140	0.82[ASN][1000 genomes]
rs2839141	0.82[ASN][1000 genomes]
rs2839144	0.83[ASN][1000 genomes]
rs2839146	0.85[ASN][1000 genomes]
rs2839155	0.84[ASN][1000 genomes]
rs2839157	0.87[ASN][1000 genomes]
rs2839161	0.81[ASN][1000 genomes]
rs35679325	0.85[ASN][1000 genomes]
rs4818828	0.84[ASN][1000 genomes]
rs4819213	0.82[ASN][1000 genomes]
rs4819214	0.83[ASN][1000 genomes]
rs4819215	0.80[ASN][1000 genomes]
rs4819217	0.84[ASN][1000 genomes]
rs4819218	0.81[ASN][1000 genomes]
rs55689527	0.82[ASN][1000 genomes]
rs62212862	0.81[ASN][1000 genomes]
rs6518278	0.87[ASN][1000 genomes]
rs6518282	0.82[ASN][1000 genomes]
rs6518285	0.83[ASN][1000 genomes]
rs7280110	0.82[ASN][1000 genomes]
rs7282841	0.83[ASN][1000 genomes]
rs9717	0.81[ASN][1000 genomes]
rs9976233	0.82[ASN][1000 genomes]
rs9979525	0.83[ASN][1000 genomes]
rs9984242	0.83[ASN][1000 genomes]
rs9984986	0.86[ASN][1000 genomes]
rs999691	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2001809	PCNT	cis	brain	BrainEAC
rs2001809	YBEY	cis	Esophagus Mucosa	GTEx
rs2001809	YBEY	cis	Esophagus Muscularis	GTEx
rs2001809	YBEY	cis	Whole Blood	GTEx
rs2001809	YBEY	cis	Thyroid	GTEx
rs2001809	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx
rs2001809	MCM3AP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr21:47606600-47639800	Strong transcription	Fetal Brain Female	brain
6	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
8	chr21:47609000-47634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr21:47610000-47637600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr21:47610000-47644000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:47611000-47633600	Weak transcription	Right Atrium	heart
12	chr21:47611600-47642400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:47611600-47643400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:47611800-47633400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr21:47611800-47634800	Strong transcription	NHDF-Ad	bronchial
16	chr21:47612000-47635600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr21:47612200-47644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:47612200-47645600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr21:47612400-47644400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:47614200-47646000	Weak transcription	Fetal Brain Male	brain
21	chr21:47614200-47646200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr21:47616200-47633200	Weak transcription	Fetal Heart	heart
23	chr21:47617000-47640400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr21:47618400-47643400	Strong transcription	NHEK	skin
25	chr21:47619200-47634600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr21:47619200-47643400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr21:47621000-47641200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr21:47622400-47634200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:47622400-47638000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:47622400-47643200	Strong transcription	Liver	Liver
31	chr21:47622400-47643400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr21:47622600-47631800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr21:47622600-47636600	Strong transcription	Colonic Mucosa	Colon
34	chr21:47622600-47637400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr21:47622600-47637600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr21:47622600-47637800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr21:47622600-47637800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr21:47622600-47637800	Strong transcription	Gastric	stomach
39	chr21:47622600-47638000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr21:47622600-47643000	Strong transcription	Ovary	ovary
41	chr21:47622600-47643400	Strong transcription	Fetal Intestine Small	intestine
42	chr21:47622800-47631400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr21:47622800-47631400	Strong transcription	Esophagus	oesophagus
44	chr21:47622800-47632000	Strong transcription	HMEC	breast
45	chr21:47622800-47633800	Strong transcription	Primary T cells from cord blood	blood
46	chr21:47622800-47636800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr21:47622800-47637600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:47622800-47638000	Strong transcription	Dnd41	blood
49	chr21:47622800-47639400	Strong transcription	Brain Germinal Matrix	brain
50	chr21:47622800-47642400	Strong transcription	Stomach Smooth Muscle	stomach

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