Variant report

Variant	rs5762777
Chromosome Location	chr22:29150044-29150045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs5752783	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs5752786	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752791	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762768	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5762776	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762783	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997397	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005862	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005863	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005864	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9608698	0.89[EUR][1000 genomes]
rs9613668	0.82[AMR][1000 genomes];0.90[EUR][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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	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
rs5762777	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29139200-29153800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:29139400-29156400	Weak transcription	Stomach Mucosa	stomach
3	chr22:29139800-29150600	Strong transcription	Fetal Stomach	stomach
4	chr22:29139800-29156000	Weak transcription	HMEC	breast
5	chr22:29140800-29152000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:29140800-29155800	Weak transcription	Fetal Brain Female	brain
7	chr22:29141000-29153200	Weak transcription	Aorta	Aorta
8	chr22:29141200-29156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:29143400-29156600	Weak transcription	Brain Substantia Nigra	brain
10	chr22:29143600-29154000	Weak transcription	Thymus	Thymus
11	chr22:29143600-29155600	Weak transcription	Gastric	stomach
12	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:29143800-29153600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr22:29143800-29155600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr22:29143800-29156000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr22:29143800-29156400	Weak transcription	Brain Angular Gyrus	brain
17	chr22:29144000-29153400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr22:29144400-29156200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr22:29144400-29156200	Weak transcription	Brain Hippocampus Middle	brain
20	chr22:29144400-29156200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr22:29144600-29150800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr22:29144600-29155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr22:29144600-29155800	Weak transcription	Brain Germinal Matrix	brain
24	chr22:29144800-29154600	Weak transcription	Right Atrium	heart
25	chr22:29145200-29154800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:29145400-29154800	Weak transcription	Left Ventricle	heart
27	chr22:29145400-29155400	Weak transcription	Colon Smooth Muscle	Colon
28	chr22:29145400-29157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr22:29145600-29155400	Weak transcription	HSMM	muscle
30	chr22:29145600-29155600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr22:29145600-29155600	Weak transcription	HSMMtube	muscle
32	chr22:29145800-29153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:29145800-29153800	Weak transcription	Fetal Thymus	thymus
34	chr22:29145800-29155800	Weak transcription	Ovary	ovary
35	chr22:29145800-29156200	Weak transcription	Spleen	Spleen
36	chr22:29145800-29156600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr22:29146000-29155400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr22:29146000-29155400	Weak transcription	HepG2	liver
40	chr22:29146000-29155600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:29146000-29155600	Weak transcription	Colonic Mucosa	Colon
42	chr22:29146000-29155800	Weak transcription	Brain Anterior Caudate	brain
43	chr22:29146000-29155800	Weak transcription	GM12878-XiMat	blood
44	chr22:29146000-29156400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr22:29146000-29156600	Weak transcription	Adipose Nuclei	Adipose
46	chr22:29146600-29156200	Weak transcription	Primary B cells from cord blood	blood
47	chr22:29146800-29150200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr22:29146800-29156600	Weak transcription	Primary T cells from cord blood	blood
49	chr22:29146800-29156600	Weak transcription	Fetal Intestine Large	intestine
50	chr22:29147000-29150400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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