Variant report

Variant	rs9975531
Chromosome Location	chr21:40033035-40033036
allele	C/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	POLR2A	chr21:40032786-40033097	MCF-7	breast:	n/a	n/a
2	EGR1	chr21:40032494-40033110	H1-hESC	embryonic stem cell:	n/a	chr21:40032687-40032700 chr21:40032692-40032702
3	HDAC2	chr21:40032516-40033158	MCF-7	breast:	n/a	n/a
4	E2F6	chr21:40032297-40033764	H1-hESC	embryonic stem cell:	n/a	chr21:40032692-40032701 chr21:40032506-40032515
5	ZNF143	chr21:40032779-40033118	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr21:40032256-40033044	ECC-1	luminal epithelium:	n/a	n/a
7	SUZ12	chr21:40031839-40033787	NT2-D1	testis:	n/a	n/a
8	EGR1	chr21:40032426-40033060	ECC-1	luminal epithelium:	n/a	chr21:40032687-40032700 chr21:40032692-40032702
9	POLR2A	chr21:40032720-40033131	ProgFib	skin:	n/a	n/a
10	POLR2A	chr21:40032902-40033619	H1-neurons	neurons:	n/a	n/a
11	MAX	chr21:40032192-40033108	ECC-1	luminal epithelium:	n/a	chr21:40032227-40032237 chr21:40032425-40032434
12	MAX	chr21:40032255-40033077	ECC-1	luminal epithelium:	n/a	chr21:40032425-40032434
13	EGR1	chr21:40032477-40033111	ECC-1	luminal epithelium:	n/a	chr21:40032687-40032700 chr21:40032692-40032702
14	HDAC2	chr21:40032388-40033119	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTBP2	chr21:40032103-40033755	H1-hESC	embryonic stem cell:	n/a	n/a
16	HA-E2F1	chr21:40032583-40033554	MCF-7	breast:	n/a	chr21:40032692-40032701
17	SIN3A	chr21:40032732-40033053	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr21:40032760-40033178	MCF-7	breast:	n/a	n/a
19	MAX	chr21:40032251-40033696	H1-hESC	embryonic stem cell:	n/a	chr21:40033420-40033427 chr21:40032425-40032434
20	ZNF263	chr21:40032382-40033668	HEK293-T-REx	kidney:	n/a	chr21:40032920-40032941 chr21:40033351-40033360
21	MAX	chr21:40032486-40033693	MCF-7	breast:	n/a	chr21:40033420-40033427
22	EGR1	chr21:40032519-40033160	MCF-7	breast:	n/a	chr21:40032687-40032700 chr21:40032692-40032702
23	POLR2A	chr21:40032604-40033159	HL-60	blood:	n/a	n/a
24	MAX	chr21:40032780-40033689	H1-hESC	embryonic stem cell:	n/a	chr21:40033420-40033427
25	E2F6	chr21:40032301-40033673	H1-hESC	embryonic stem cell:	n/a	chr21:40032692-40032701 chr21:40032506-40032515

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40032723..40034705-chr21:40552796..40555245,2	MCF-7	breast:

Variant related genes	Relation type
ERG	TF binding region
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015069	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1015070	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1540015	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1540016	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836613	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836619	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836620	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs458783	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs459813	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs460112	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460843	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs460947	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs461488	0.97[EUR][1000 genomes]
rs461592	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463269	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs463501	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs463530	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs465004	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs465327	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62217514	0.91[EUR][1000 genomes]
rs6517476	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132920	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8134664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9647180	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs994003	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398749	chr21:40030382-40034780	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3440316	chr21:40031607-40034455	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40028800-40034400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr21:40029800-40034600	Active TSS	Aorta	Aorta
3	chr21:40031200-40034400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr21:40031400-40033800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr21:40031800-40033200	Bivalent/Poised TSS	Osteobl	bone
6	chr21:40031800-40033600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
7	chr21:40031800-40034000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr21:40031800-40034000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr21:40031800-40034000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr21:40031800-40034200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr21:40032000-40033200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
12	chr21:40032000-40033200	Flanking Bivalent TSS/Enh	Thymus	Thymus
13	chr21:40032000-40033600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:40032000-40033800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr21:40032000-40033800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr21:40032000-40033800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
17	chr21:40032000-40034000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr21:40032000-40034000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr21:40032200-40033200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:40032200-40033400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr21:40032200-40033400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:40032200-40033400	Active TSS	Right Atrium	heart
23	chr21:40032200-40033600	Bivalent Enhancer	Fetal Brain Male	brain
24	chr21:40032200-40033600	Flanking Bivalent TSS/Enh	HMEC	breast
25	chr21:40032200-40033800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr21:40032200-40033800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr21:40032200-40033800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr21:40032200-40034200	Active TSS	Ovary	ovary
29	chr21:40032400-40033200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:40032400-40033200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr21:40032400-40033200	Bivalent/Poised TSS	NH-A	brain
32	chr21:40032400-40033400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr21:40032400-40033400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:40032400-40033400	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr21:40032400-40033400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr21:40032400-40033400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr21:40032400-40033400	Bivalent/Poised TSS	Fetal Brain Female	brain
38	chr21:40032400-40033600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr21:40032400-40033600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
40	chr21:40032400-40033600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:40032400-40033600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
42	chr21:40032400-40033600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr21:40032400-40033600	Bivalent/Poised TSS	Psoas Muscle	Psoas
44	chr21:40032400-40033800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr21:40032400-40033800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr21:40032400-40033800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr21:40032400-40033800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr21:40032400-40033800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr21:40032400-40033800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
50	chr21:40032400-40033800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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