Variant report

Variant	rs5762882
Chromosome Location	chr22:29290680-29290681
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29290300..29292504-chr22:29426494..29429452,2	K562	blood:
2	chr22:29287874..29289699-chr22:29289743..29291246,2	K562	blood:
3	chr22:29289372..29291896-chr22:29597783..29600686,2	MCF-7	breast:
4	chr22:29289506..29292443-chr22:29294897..29296592,2	K562	blood:

Variant related genes	Relation type
ENSG00000177993	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1065497	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12165962	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs1318025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318026	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132528	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132529	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132531	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132536	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132543	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132548	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015500	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2064261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097461	0.84[JPT][hapmap]
rs2213645	0.95[JPT][hapmap]
rs2239815	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs2239828	0.96[CEU][hapmap]
rs2269577	0.84[JPT][hapmap]
rs2347447	0.89[JPT][hapmap]
rs3788409	0.89[JPT][hapmap]
rs469990	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469991	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469992	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4822998	0.94[JPT][hapmap]
rs5752809	0.84[JPT][hapmap]
rs5752812	0.84[JPT][hapmap]
rs5752826	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap]
rs5762788	0.89[JPT][hapmap]
rs5762795	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762870	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5762874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762881	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762936	0.95[JPT][hapmap]
rs5997408	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs5997412	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap]
rs6005915	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6005936	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6519766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715531	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287806	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs7287918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763073	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8142067	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5762882	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29281400-29294600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr22:29281400-29295200	Weak transcription	Brain Hippocampus Middle	brain
3	chr22:29281600-29292600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:29282000-29291400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr22:29282200-29295000	Weak transcription	Brain Substantia Nigra	brain
6	chr22:29283400-29294200	Weak transcription	Aorta	Aorta
7	chr22:29283400-29299000	Weak transcription	Fetal Stomach	stomach
8	chr22:29284200-29292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr22:29286000-29299000	Weak transcription	Ovary	ovary
10	chr22:29286200-29291600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr22:29286800-29297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29287400-29291200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr22:29288000-29290800	Enhancers	Duodenum Mucosa	Duodenum
14	chr22:29288000-29301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr22:29288400-29291400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr22:29288400-29295000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29288400-29299000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:29288400-29299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr22:29288600-29292600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr22:29288600-29292600	Weak transcription	Fetal Kidney	kidney
21	chr22:29288600-29292600	Weak transcription	HSMM	muscle
22	chr22:29288600-29293600	Weak transcription	Liver	Liver
23	chr22:29288600-29294600	Weak transcription	Colon Smooth Muscle	Colon
24	chr22:29288600-29295000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr22:29288600-29296200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:29288600-29298600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr22:29288800-29292600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:29288800-29292600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr22:29289600-29291800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr22:29289800-29291200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr22:29289800-29291200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr22:29290000-29291200	Enhancers	Fetal Heart	heart
33	chr22:29290000-29291400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr22:29290000-29291400	Genic enhancers	HepG2	liver
35	chr22:29290000-29291400	Enhancers	HMEC	breast
36	chr22:29290000-29291800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr22:29290000-29296800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:29290200-29290800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:29290200-29291000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr22:29290200-29291000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr22:29290200-29291200	Genic enhancers	Fetal Intestine Small	intestine
42	chr22:29290200-29291200	Enhancers	Left Ventricle	heart
43	chr22:29290200-29291800	Enhancers	Primary hematopoietic stem cells	blood
44	chr22:29290400-29290800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr22:29290400-29290800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr22:29290400-29290800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr22:29290400-29290800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29290400-29290800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr22:29290400-29290800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:29290400-29290800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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