Variant report

Variant	rs2823479
Chromosome Location	chr21:17142181-17142182
allele	A/T
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	ZNF274	chr21:17141538-17142181	K562	blood:	n/a	n/a
2	KAP1	chr21:17142061-17142500	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:17100962..17103706-chr21:17140698..17142890,2	MCF-7	breast:
2	chr21:17141263..17145457-chr21:17148743..17151657,3	MCF-7	breast:
3	chr21:17141227..17143444-chr21:17164471..17166670,2	K562	blood:

Variant related genes	Relation type
USP25	TF binding region
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11909953	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs13347185	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17241402	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17307156	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1986788	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2183553	0.81[ASN][1000 genomes]
rs2823464	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2823467	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823473	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2823488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28484960	0.82[ASN][1000 genomes]
rs28553297	0.82[ASN][1000 genomes]
rs28730511	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55804442	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58134477	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58683309	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60174740	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517612	1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7277813	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8128335	1.00[CEU][hapmap]
rs8130607	0.92[CHB][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8132755	0.82[ASN][1000 genomes]
rs926612	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9305754	0.93[CHB][hapmap]
rs9680115	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9977019	0.93[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
2	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
3	chr21:17122600-17142800	Weak transcription	Hela-S3	cervix
4	chr21:17125800-17153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:17126800-17147600	Weak transcription	Placenta	Placenta
6	chr21:17127000-17147400	Weak transcription	HSMMtube	muscle
7	chr21:17127000-17152800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr21:17127200-17153400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:17127400-17146200	Weak transcription	NHDF-Ad	bronchial
10	chr21:17127400-17147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:17127400-17153400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr21:17127600-17145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr21:17127800-17152800	Weak transcription	Fetal Intestine Large	intestine
14	chr21:17130800-17156800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr21:17132800-17153400	Weak transcription	Spleen	Spleen
16	chr21:17133800-17145800	Weak transcription	Colon Smooth Muscle	Colon
17	chr21:17133800-17149400	Weak transcription	Small Intestine	intestine
18	chr21:17134000-17143600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr21:17134000-17143600	Weak transcription	Gastric	stomach
20	chr21:17134000-17147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr21:17134000-17152400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr21:17134000-17153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:17134200-17142200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr21:17134200-17143400	Weak transcription	Right Atrium	heart
25	chr21:17134200-17143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr21:17134200-17153000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr21:17134200-17153400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr21:17134200-17154000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr21:17134400-17143600	Weak transcription	Lung	lung
30	chr21:17134400-17153200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:17134600-17143800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr21:17135000-17145000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr21:17135000-17152600	Weak transcription	Primary T cells from cord blood	blood
34	chr21:17135000-17153000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr21:17135000-17153400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr21:17135000-17153600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr21:17135200-17142400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr21:17135200-17153000	Weak transcription	Fetal Muscle Leg	muscle
39	chr21:17135400-17153200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr21:17135600-17153200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr21:17135800-17147200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr21:17136000-17145400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr21:17136600-17148400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr21:17136600-17153200	Weak transcription	Thymus	Thymus
45	chr21:17137200-17142800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr21:17137600-17144200	Strong transcription	GM12878-XiMat	blood
47	chr21:17137600-17145400	Weak transcription	Fetal Stomach	stomach
48	chr21:17138200-17142400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr21:17138200-17144200	Strong transcription	Dnd41	blood
50	chr21:17138600-17152800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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