Variant report

Variant	rs2239828
Chromosome Location	chr22:29358802-29358803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29357505..29361534-chr22:29364431..29368155,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs132531	0.96[CEU][hapmap]
rs132533	0.96[CEU][hapmap]
rs132536	0.92[CEU][hapmap]
rs132548	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs132561	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2064261	0.96[CEU][hapmap]
rs2213645	0.85[JPT][hapmap]
rs469990	0.92[CEU][hapmap]
rs469991	0.96[CEU][hapmap]
rs4822998	0.83[JPT][hapmap]
rs5762874	0.96[CEU][hapmap]
rs5762881	0.96[CEU][hapmap]
rs5762882	0.96[CEU][hapmap]
rs5997408	0.80[CEU][hapmap]
rs6519766	0.96[CEU][hapmap]
rs7287918	0.96[CEU][hapmap]
rs9620841	0.96[CEU][hapmap]
rs9625619	0.96[CEU][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	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
rs2239828	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29348200-29365000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr22:29348800-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:29349200-29365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29349200-29371800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:29349200-29371800	Weak transcription	HSMM	muscle
6	chr22:29349600-29359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:29349800-29360400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr22:29350000-29363000	Weak transcription	Liver	Liver
9	chr22:29350000-29372800	Weak transcription	Aorta	Aorta
10	chr22:29350400-29361000	Weak transcription	Ovary	ovary
11	chr22:29351400-29362200	Genic enhancers	HepG2	liver
12	chr22:29352400-29359600	Weak transcription	Gastric	stomach
13	chr22:29352800-29360400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:29353000-29359200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:29354800-29360600	Weak transcription	Right Ventricle	heart
16	chr22:29354800-29364800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr22:29354800-29365600	Weak transcription	Lung	lung
18	chr22:29355200-29365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr22:29355400-29360400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:29355400-29360800	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:29355400-29363600	Weak transcription	Fetal Stomach	stomach
22	chr22:29355400-29364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr22:29355400-29365000	Weak transcription	Right Atrium	heart
24	chr22:29355400-29365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr22:29355400-29372800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr22:29355800-29364600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:29356000-29359000	Weak transcription	Pancreas	Pancrea
28	chr22:29356000-29360400	Weak transcription	Esophagus	oesophagus
29	chr22:29356000-29365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr22:29356800-29366400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr22:29357000-29359400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr22:29357200-29359400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:29357200-29360400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr22:29357400-29359000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr22:29357400-29359600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:29357400-29360000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:29357400-29360600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:29357600-29359200	Enhancers	Brain Substantia Nigra	brain
39	chr22:29357600-29360200	Enhancers	Brain Anterior Caudate	brain
40	chr22:29357600-29360600	Weak transcription	Psoas Muscle	Psoas
41	chr22:29357600-29364800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr22:29357800-29359200	Weak transcription	Brain Hippocampus Middle	brain
43	chr22:29357800-29360000	Enhancers	HSMMtube	muscle
44	chr22:29357800-29360200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr22:29357800-29364800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr22:29358000-29360600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr22:29358000-29360600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr22:29358200-29359000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:29358200-29359000	Enhancers	Fetal Intestine Small	intestine
50	chr22:29358200-29359600	Enhancers	Fetal Intestine Large	intestine

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