Variant report

Variant	rs2822520
Chromosome Location	chr21:15646060-15646061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr21:15646004-15646549	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr21:15645936-15646477	PBDE	blood:	n/a	n/a
3	USF1	chr21:15645976-15646478	ECC-1	luminal epithelium:	n/a	n/a
4	HA-E2F1	chr21:15646010-15646915	MCF-7	breast:	n/a	n/a
5	UBTF	chr21:15646047-15646758	K562	blood:	n/a	n/a
6	NFIC	chr21:15645966-15646712	ECC-1	luminal epithelium:	n/a	n/a
7	FOXA1	chr21:15646026-15646457	T-47D	breast:	n/a	n/a
8	MAX	chr21:15645942-15646480	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr21:15645944-15646657	ECC-1	luminal epithelium:	n/a	chr21:15646034-15646048 chr21:15646035-15646044
10	SIN3A	chr21:15645935-15646789	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF1	chr21:15645928-15646499	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr21:15645952-15646304	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr21:15645919-15646729	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr21:15646018-15646419	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:15645251..15647400-chr21:15754351..15756122,2	K562	blood:

No data

Variant related genes	Relation type
ABCC13	TF binding region
ENSG00000155304	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs108885	0.82[CHB][hapmap]
rs11701767	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1739487	0.84[CHB][hapmap]
rs2110153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822521	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822548	0.82[JPT][hapmap]
rs28413131	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367249	0.86[CHD][hapmap]
rs369923	0.84[CHB][hapmap]
rs385758	0.92[CHB][hapmap]
rs389338	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs389493	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs423169	0.92[CHB][hapmap];0.90[CHD][hapmap]
rs437521	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs452794	0.83[ASN][1000 genomes]
rs62230076	0.94[ASN][1000 genomes]
rs718670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718672	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs718673	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73163620	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305276	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9808686	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9975020	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9979345	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869466	chr21:15482572-15683385	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv520538	chr21:15615220-15660539	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1062532	chr21:15616629-15654501	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1067478	chr21:15616629-15657107	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1062862	chr21:15620391-15649232	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1062500	chr21:15620391-15657107	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv915906	chr21:15620908-15651744	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv544374	chr21:15624517-15656011	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1066930	chr21:15626232-15724630	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv459095	chr21:15626660-15698808	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv587044	chr21:15626660-15698808	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv470878	chr21:15630812-15698808	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822520	ABCC13	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15645200-15646200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr21:15645800-15646400	Enhancers	Brain Germinal Matrix	brain
3	chr21:15645800-15647000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr21:15645800-15647400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr21:15646000-15646200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr21:15646000-15646200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr21:15646000-15646200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:15646000-15646200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr21:15646000-15646200	Enhancers	Primary hematopoietic stem cells	blood
10	chr21:15646000-15646200	Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr21:15646000-15646200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
12	chr21:15646000-15646200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
13	chr21:15646000-15646200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
14	chr21:15646000-15646200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
15	chr21:15646000-15646200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr21:15646000-15646200	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr21:15646000-15646200	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr21:15646000-15646200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr21:15646000-15646200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr21:15646000-15646200	Active TSS	Gastric	stomach
21	chr21:15646000-15646200	Enhancers	Right Ventricle	heart
22	chr21:15646000-15646200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr21:15646000-15646200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr21:15646000-15646200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
25	chr21:15646000-15646200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
26	chr21:15646000-15646400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
27	chr21:15646000-15646400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:15646000-15646400	Flanking Active TSS	Liver	Liver
29	chr21:15646000-15646400	Flanking Active TSS	Esophagus	oesophagus
30	chr21:15646000-15646400	Bivalent Enhancer	Fetal Brain Male	brain
31	chr21:15646000-15646400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
32	chr21:15646000-15646400	Flanking Active TSS	Left Ventricle	heart
33	chr21:15646000-15646400	Active TSS	Psoas Muscle	Psoas
34	chr21:15646000-15646400	Flanking Bivalent TSS/Enh	HMEC	breast
35	chr21:15646000-15646600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr21:15646000-15646600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr21:15646000-15646600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr21:15646000-15646600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr21:15646000-15646600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr21:15646000-15646600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr21:15646000-15646600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr21:15646000-15646600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr21:15646000-15646600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:15646000-15646600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
45	chr21:15646000-15646600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr21:15646000-15646600	Flanking Bivalent TSS/Enh	Placenta	Placenta
47	chr21:15646000-15646600	Flanking Active TSS	Pancreas	Pancrea
48	chr21:15646000-15646600	Active TSS	Right Atrium	heart
49	chr21:15646000-15646600	Bivalent/Poised TSS	HepG2	liver
50	chr21:15646000-15646600	Flanking Active TSS	K562	blood

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