Variant report

Variant	rs5752813
Chromosome Location	chr22:29226570-29226571
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29226187..29227973-chr22:29425770..29428357,2	MCF-7	breast:
2	chr22:29218595..29221875-chr22:29223900..29227184,8	MCF-7	breast:
3	chr22:29226520..29228881-chr22:29235030..29237241,2	K562	blood:
4	chr22:29136502..29138198-chr22:29224154..29227146,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177993	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12628211	0.96[ASN][1000 genomes]
rs2097461	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239815	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269577	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347447	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2881635	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35259224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3788409	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752795	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752798	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752801	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752804	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752807	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752809	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752812	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762784	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762788	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762795	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762803	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5762815	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762825	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762853	0.85[ASN][1000 genomes]
rs5762854	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762863	0.85[ASN][1000 genomes]
rs5762864	0.85[ASN][1000 genomes]
rs5762865	0.83[EUR][1000 genomes]
rs5762870	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5997408	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005867	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005869	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6005872	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005881	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005892	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005916	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005927	0.82[ASN][1000 genomes]
rs6005929	0.84[ASN][1000 genomes]
rs7287124	0.96[ASN][1000 genomes]
rs7287806	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763073	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8137969	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625566	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9625588	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5752813	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 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	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
6	chr22:29215600-29231600	Weak transcription	Right Ventricle	heart
7	chr22:29216000-29227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:29216000-29231600	Weak transcription	Placenta	Placenta
9	chr22:29216000-29232800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr22:29216000-29233800	Weak transcription	Left Ventricle	heart
11	chr22:29216000-29238600	Weak transcription	Spleen	Spleen
12	chr22:29216200-29227600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr22:29218200-29231800	Weak transcription	Gastric	stomach
14	chr22:29219400-29234800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:29219600-29231800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr22:29223000-29226600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:29223200-29227800	Weak transcription	Fetal Stomach	stomach
18	chr22:29224000-29237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr22:29224200-29228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr22:29225200-29226600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr22:29225200-29226600	Enhancers	Fetal Intestine Large	intestine
22	chr22:29225200-29227200	Enhancers	Fetal Intestine Small	intestine
23	chr22:29225400-29242000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr22:29225600-29226600	Enhancers	Fetal Muscle Leg	muscle
25	chr22:29225600-29226600	Flanking Active TSS	HepG2	liver
26	chr22:29225800-29227000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr22:29225800-29227200	Enhancers	Liver	Liver
28	chr22:29225800-29228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr22:29225800-29229000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:29225800-29231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr22:29225800-29231800	Weak transcription	HSMM	muscle
32	chr22:29225800-29233000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr22:29226000-29228200	Weak transcription	Brain Anterior Caudate	brain
34	chr22:29226000-29229000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr22:29226000-29229000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr22:29226000-29229200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr22:29226000-29229600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr22:29226000-29230000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr22:29226000-29231600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr22:29226000-29233000	Weak transcription	Dnd41	blood
41	chr22:29226000-29248800	Weak transcription	Primary T cells from cord blood	blood
42	chr22:29226200-29227800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr22:29226200-29230000	Weak transcription	Fetal Thymus	thymus
44	chr22:29226200-29230200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr22:29226200-29234600	Weak transcription	Brain Substantia Nigra	brain
46	chr22:29226200-29234800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr22:29226200-29239600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr22:29226200-29242800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr22:29226400-29227400	Weak transcription	Stomach Mucosa	stomach
50	chr22:29226400-29231600	Weak transcription	Pancreas	Pancrea

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