Variant report

Variant	rs233900
Chromosome Location	chr21:28322773-28322774
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	POLR2A	chr21:28322683-28322798	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MIR4759	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1497288	1.00[ASN][1000 genomes]
rs151056	0.84[EUR][1000 genomes]
rs151059	0.90[EUR][1000 genomes]
rs162488	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162490	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162491	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162492	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162493	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162494	0.90[EUR][1000 genomes]
rs162496	0.84[EUR][1000 genomes]
rs162497	0.84[EUR][1000 genomes]
rs162498	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162499	0.84[EUR][1000 genomes]
rs162501	1.00[ASN][1000 genomes]
rs162503	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162504	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162505	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162506	0.85[AMR][1000 genomes]
rs162507	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162510	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162516	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162520	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162521	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162531	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162532	0.89[EUR][1000 genomes]
rs162533	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162534	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162535	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162536	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162537	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162540	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162541	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229045	0.84[EUR][1000 genomes]
rs229046	0.84[EUR][1000 genomes]
rs229049	0.90[EUR][1000 genomes]
rs229050	0.90[EUR][1000 genomes]
rs229060	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229061	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229063	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229064	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229069	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229071	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229076	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229078	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229079	0.83[EUR][1000 genomes]
rs229085	1.00[ASN][1000 genomes]
rs229087	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229088	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229089	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229090	0.85[EUR][1000 genomes]
rs229091	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229093	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229095	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229097	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229103	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229109	0.83[EUR][1000 genomes]
rs229110	0.80[EUR][1000 genomes]
rs233897	0.91[EUR][1000 genomes]
rs233898	0.91[EUR][1000 genomes]
rs233899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830556	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830584	0.85[EUR][1000 genomes]
rs2830589	0.90[EUR][1000 genomes]
rs389125	0.82[EUR][1000 genomes]
rs431134	0.84[EUR][1000 genomes]
rs457947	1.00[ASN][1000 genomes]
rs4817147	1.00[ASN][1000 genomes]
rs7281968	0.85[EUR][1000 genomes]
rs73358063	1.00[ASN][1000 genomes]
rs73358075	1.00[ASN][1000 genomes]
rs73899348	1.00[ASN][1000 genomes]
rs8127064	1.00[ASN][1000 genomes]
rs8131204	1.00[ASN][1000 genomes]
rs8992	1.00[ASN][1000 genomes]
rs9647124	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28293000-28334800	Weak transcription	Hela-S3	cervix
2	chr21:28306600-28333600	Weak transcription	Fetal Intestine Large	intestine
3	chr21:28307600-28324800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr21:28309600-28337200	Weak transcription	Fetal Heart	heart
5	chr21:28317000-28330400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr21:28318600-28324800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr21:28318600-28327000	Weak transcription	Psoas Muscle	Psoas
8	chr21:28318600-28333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr21:28318600-28336600	Weak transcription	Left Ventricle	heart
10	chr21:28318800-28324600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:28319200-28334200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr21:28319400-28323200	Weak transcription	Fetal Brain Male	brain
13	chr21:28319400-28326600	Weak transcription	Brain Germinal Matrix	brain
14	chr21:28319400-28328600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr21:28319600-28326600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr21:28319600-28328400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:28319600-28334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:28319800-28324800	Weak transcription	NHLF	lung
19	chr21:28319800-28326000	Weak transcription	Fetal Brain Female	brain
20	chr21:28320000-28324000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr21:28320000-28324600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:28320400-28323800	Enhancers	Dnd41	blood
23	chr21:28320800-28323800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:28320800-28326600	Weak transcription	Ovary	ovary
25	chr21:28321000-28323000	Strong transcription	Adipose Nuclei	Adipose
26	chr21:28321000-28323000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr21:28321000-28324400	Weak transcription	Fetal Kidney	kidney
28	chr21:28321000-28325000	Strong transcription	HSMMtube	muscle
29	chr21:28321000-28326400	Strong transcription	HSMM	muscle
30	chr21:28321000-28326800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr21:28321000-28328400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:28321200-28323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr21:28321600-28322800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr21:28321600-28324400	Strong transcription	Fetal Muscle Leg	muscle
35	chr21:28322000-28327400	Strong transcription	Osteobl	bone
36	chr21:28322200-28324800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:28322400-28322800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr21:28322400-28324000	Weak transcription	NHDF-Ad	bronchial
39	chr21:28322400-28324400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr21:28322600-28323800	Weak transcription	Fetal Lung	lung
41	chr21:28322600-28328400	Weak transcription	Fetal Stomach	stomach

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