Variant report

Variant	rs5752888
Chromosome Location	chr22:29641551-29641552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29598605..29599258-chr22:29640938..29642145,5	MCF-7	breast:
2	chr22:29598263..29599277-chr22:29640793..29642655,17	MCF-7	breast:
3	chr22:29251341..29252226-chr22:29641199..29642209,3	K562	blood:
4	chr22:29411148..29412690-chr22:29641061..29643076,2	K562	blood:
5	chr22:29601618..29602130-chr22:29641210..29642068,2	MCF-7	breast:
6	chr22:29601718..29602561-chr22:29641280..29642104,3	MCF-7	breast:
7	chr22:29639575..29642447-chr22:29663605..29665406,2	K562	blood:
8	chr22:29436679..29437351-chr22:29641273..29642121,2	K562	blood:
9	chr22:29600704..29601509-chr22:29641190..29641939,2	MCF-7	breast:
10	chr22:29552265..29553268-chr22:29641211..29642160,5	MCF-7	breast:
11	chr22:29550189..29551060-chr22:29641253..29641991,3	MCF-7	breast:
12	chr22:29640165..29643423-chr22:29644673..29648917,5	K562	blood:
13	chr22:29640909..29643283-chr22:29659870..29662528,2	K562	blood:
14	chr22:29473166..29474828-chr22:29640994..29643456,2	K562	blood:
15	chr22:29598698..29599406-chr22:29641204..29641781,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000182944	Chromatin interaction
ENSG00000186998	Chromatin interaction
ENSG00000100263	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12166644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12628709	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16987313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765295	0.93[ASN][1000 genomes]
rs3765297	0.94[ASN][1000 genomes]
rs3765300	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3950176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752895	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763080	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5763084	0.98[ASN][1000 genomes]
rs5763087	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763094	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763110	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763111	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6006068	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6006072	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006073	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006074	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006075	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv275243	chr22:29638470-29642365	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29622000-29655200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29622000-29655800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:29622400-29656600	Weak transcription	Colonic Mucosa	Colon
4	chr22:29629000-29659400	Weak transcription	Brain Anterior Caudate	brain
5	chr22:29629600-29655400	Weak transcription	Liver	Liver
6	chr22:29629600-29655400	Weak transcription	Gastric	stomach
7	chr22:29633600-29654400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:29634600-29655200	Weak transcription	Brain Angular Gyrus	brain
9	chr22:29638400-29655200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:29639000-29655200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr22:29639200-29643200	Strong transcription	Fetal Stomach	stomach
12	chr22:29639400-29654200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr22:29639600-29642000	Genic enhancers	Dnd41	blood
14	chr22:29639800-29641600	Enhancers	Thymus	Thymus
15	chr22:29639800-29642000	Enhancers	Fetal Thymus	thymus
16	chr22:29639800-29656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr22:29640200-29650200	Weak transcription	Brain Germinal Matrix	brain
18	chr22:29640400-29641800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr22:29640400-29642000	Weak transcription	Fetal Kidney	kidney
20	chr22:29640400-29651200	Weak transcription	Lung	lung
21	chr22:29640800-29641600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:29640800-29641600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr22:29640800-29641600	Genic enhancers	Spleen	Spleen
24	chr22:29641000-29641600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:29641000-29641800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:29641000-29642600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:29641200-29641600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr22:29641200-29641600	Enhancers	Fetal Brain Male	brain
29	chr22:29641200-29641600	Weak transcription	Fetal Lung	lung
30	chr22:29641200-29641800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr22:29641200-29642000	Enhancers	Colon Smooth Muscle	Colon
32	chr22:29641200-29642400	Strong transcription	Fetal Brain Female	brain
33	chr22:29641200-29642400	Genic enhancers	Fetal Intestine Large	intestine
34	chr22:29641200-29642600	Genic enhancers	Fetal Intestine Small	intestine
35	chr22:29641400-29641600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:29641400-29641600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr22:29641400-29641600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr22:29641400-29641600	Enhancers	Ovary	ovary
39	chr22:29641400-29641600	Enhancers	Pancreas	Pancrea
40	chr22:29641400-29641600	Enhancers	GM12878-XiMat	blood
41	chr22:29641400-29641800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr22:29641400-29642000	Enhancers	Fetal Muscle Leg	muscle
43	chr22:29641400-29642200	Enhancers	Stomach Smooth Muscle	stomach
44	chr22:29641400-29642400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr22:29641400-29642600	Enhancers	Fetal Muscle Trunk	muscle
46	chr22:29641400-29642800	Enhancers	HepG2	liver
47	chr22:29641400-29643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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