Variant report

Variant	rs5752809
Chromosome Location	chr22:29225500-29225501
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29188183..29190691-chr22:29223821..29225664,2	K562	blood:
2	chr22:28996205..28996831-chr22:29225489..29226015,2	MCF-7	breast:
3	chr22:29168719..29169263-chr22:29225285..29225962,2	MCF-7	breast:
4	chr22:29221484..29225930-chr22:29227534..29231329,4	MCF-7	breast:
5	chr22:29225150..29226028-chr22:29251651..29252215,2	K562	blood:
6	chr22:29137501..29139730-chr22:29224084..29225610,2	MCF-7	breast:
7	chr22:28996270..28996801-chr22:29225446..29225968,2	MCF-7	breast:
8	chr22:29218595..29221875-chr22:29223900..29227184,8	MCF-7	breast:
9	chr22:29145130..29148116-chr22:29224104..29225824,2	MCF-7	breast:
10	chr22:29136502..29138198-chr22:29224154..29227146,2	MCF-7	breast:
11	chr22:28995974..28997136-chr22:29225078..29225924,5	K562	blood:
12	chr22:29185898..29186822-chr22:29225037..29225561,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12165962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12628211	0.98[ASN][1000 genomes]
rs132531	0.89[JPT][hapmap]
rs132533	0.84[JPT][hapmap]
rs132536	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs132539	0.82[CEU][hapmap]
rs132548	0.89[JPT][hapmap]
rs2064261	0.89[JPT][hapmap]
rs2097461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2213645	0.84[JPT][hapmap]
rs2239815	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881635	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35259224	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs469989	0.86[CEU][hapmap]
rs469990	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap]
rs469991	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs4822998	0.82[JPT][hapmap]
rs5752795	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752798	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752801	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752804	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752807	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752813	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762795	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762803	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5762815	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762824	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762825	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762853	0.87[ASN][1000 genomes]
rs5762854	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762859	0.82[ASN][1000 genomes]
rs5762863	0.87[ASN][1000 genomes]
rs5762864	0.87[ASN][1000 genomes]
rs5762865	0.83[EUR][1000 genomes]
rs5762867	0.81[ASN][1000 genomes]
rs5762870	0.81[EUR][1000 genomes]
rs5762874	0.84[JPT][hapmap]
rs5762881	0.84[JPT][hapmap]
rs5762882	0.84[JPT][hapmap]
rs5762936	0.84[JPT][hapmap]
rs5997408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005867	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005869	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005872	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005881	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005892	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005915	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6005916	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005927	0.84[ASN][1000 genomes]
rs6005929	0.86[ASN][1000 genomes]
rs6519766	0.89[JPT][hapmap]
rs7287124	0.98[ASN][1000 genomes]
rs7287806	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287918	0.89[JPT][hapmap]
rs763073	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8137969	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620841	0.89[JPT][hapmap]
rs9625566	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625588	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625619	0.84[JPT][hapmap]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5752809		cis	Lymphoblastoid	GTEx
rs5752809	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
3	chr22:29198800-29230800	Weak transcription	NHEK	skin
4	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr22:29205400-29225600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr22:29211800-29225600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
8	chr22:29215400-29225600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr22:29215600-29225600	Weak transcription	Fetal Muscle Leg	muscle
10	chr22:29215600-29231600	Weak transcription	Right Ventricle	heart
11	chr22:29215800-29225600	Weak transcription	Adipose Nuclei	Adipose
12	chr22:29216000-29227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:29216000-29231600	Weak transcription	Placenta	Placenta
14	chr22:29216000-29232800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr22:29216000-29233800	Weak transcription	Left Ventricle	heart
16	chr22:29216000-29238600	Weak transcription	Spleen	Spleen
17	chr22:29216200-29227600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr22:29218200-29231800	Weak transcription	Gastric	stomach
19	chr22:29219200-29225600	Weak transcription	Pancreas	Pancrea
20	chr22:29219400-29225600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr22:29219400-29234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr22:29219600-29231800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:29219800-29225600	Weak transcription	Fetal Lung	lung
24	chr22:29223000-29226000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr22:29223000-29226600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:29223200-29227800	Weak transcription	Fetal Stomach	stomach
27	chr22:29223400-29225600	Enhancers	Dnd41	blood
28	chr22:29223400-29226200	Enhancers	Fetal Thymus	thymus
29	chr22:29224000-29237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr22:29224200-29226000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr22:29224200-29228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr22:29224400-29226000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr22:29224600-29226000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr22:29225000-29225600	Enhancers	HepG2	liver
35	chr22:29225000-29225800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr22:29225000-29225800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr22:29225000-29225800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr22:29225000-29225800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr22:29225000-29225800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr22:29225000-29226000	Enhancers	Primary T cells from cord blood	blood
41	chr22:29225000-29226000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr22:29225000-29226000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr22:29225000-29226000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr22:29225000-29226000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr22:29225000-29226000	Enhancers	Thymus	Thymus
46	chr22:29225000-29226400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr22:29225200-29225600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:29225200-29225600	Enhancers	Duodenum Mucosa	Duodenum
49	chr22:29225200-29225600	Enhancers	Stomach Mucosa	stomach
50	chr22:29225200-29225600	Enhancers	GM12878-XiMat	blood

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