Variant report

Variant	rs1318025
Chromosome Location	chr22:29283757-29283758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29280624..29284164-chr22:29307760..29311501,3	MCF-7	breast:
2	chr22:29277392..29281683-chr22:29281887..29284497,5	MCF-7	breast:
3	chr22:29278902..29281359-chr22:29283717..29285829,4	K562	blood:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1065497	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1318026	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132529	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132531	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132533	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132536	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132543	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132548	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015500	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2064261	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469990	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469991	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469992	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752826	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762870	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762874	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762877	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762881	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762882	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997412	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005936	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6519766	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715531	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8136297	0.81[EUR][1000 genomes]
rs8137262	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8142067	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620841	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625619	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	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
3	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
4	nsv3589	chr22:29265164-29288935	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1318025	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29281000-29287600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr22:29281200-29287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:29281200-29288000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:29281400-29285600	Weak transcription	Ovary	ovary
5	chr22:29281400-29287200	Weak transcription	Left Ventricle	heart
6	chr22:29281400-29287400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr22:29281400-29287400	Weak transcription	Psoas Muscle	Psoas
8	chr22:29281400-29288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:29281400-29288000	Weak transcription	Lung	lung
10	chr22:29281400-29290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr22:29281400-29290400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:29281400-29290400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr22:29281400-29290400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr22:29281400-29294600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr22:29281400-29295200	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:29281600-29284000	Enhancers	Fetal Intestine Small	intestine
17	chr22:29281600-29284600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr22:29281600-29292600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr22:29281800-29283800	Weak transcription	Fetal Brain Female	brain
20	chr22:29281800-29284200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr22:29281800-29284400	Enhancers	Fetal Intestine Large	intestine
22	chr22:29282000-29283800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:29282000-29284000	Enhancers	Stomach Mucosa	stomach
24	chr22:29282000-29284200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr22:29282000-29290400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:29282000-29291400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:29282200-29284000	Weak transcription	Adipose Nuclei	Adipose
28	chr22:29282200-29284200	Flanking Active TSS	HepG2	liver
29	chr22:29282200-29284600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:29282200-29284600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr22:29282200-29284800	Enhancers	Liver	Liver
32	chr22:29282200-29285400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr22:29282200-29287000	Weak transcription	Fetal Heart	heart
34	chr22:29282200-29287400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr22:29282200-29287600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:29282200-29287800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:29282200-29288000	Weak transcription	Right Ventricle	heart
38	chr22:29282200-29288200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:29282200-29290400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr22:29282200-29295000	Weak transcription	Brain Substantia Nigra	brain
41	chr22:29282400-29284400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:29282400-29287600	Weak transcription	HMEC	breast
43	chr22:29282400-29287800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr22:29282400-29288000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr22:29282400-29290400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr22:29282600-29284400	Enhancers	Brain Anterior Caudate	brain
47	chr22:29282800-29284400	Enhancers	Fetal Lung	lung
48	chr22:29282800-29285400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr22:29283000-29285600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr22:29283000-29287600	Weak transcription	NHEK	skin

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