Variant report

Variant	rs5762879
Chromosome Location	chr22:29286180-29286181
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	chr22:29278420..29281129-chr22:29285869..29288774,2	K562	blood:
2	chr22:29283926..29288290-chr22:29291343..29295207,5	K562	blood:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs5752810	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs5752815	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs5752822	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762839	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs5762848	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs5762873	0.92[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5762879	XBP1	cis	cerebellum	SCAN
rs5762879	SUSD2	cis	parietal	SCAN
rs5762879	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs5762879	MN1	cis	cerebellum	SCAN

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	chr22:29281400-29287200	Weak transcription	Left Ventricle	heart
5	chr22:29281400-29287400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:29281400-29287400	Weak transcription	Psoas Muscle	Psoas
7	chr22:29281400-29288000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:29281400-29288000	Weak transcription	Lung	lung
9	chr22:29281400-29290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:29281400-29290400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:29281400-29290400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr22:29281400-29290400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr22:29281400-29294600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr22:29281400-29295200	Weak transcription	Brain Hippocampus Middle	brain
15	chr22:29281600-29292600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:29282000-29290400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr22:29282000-29291400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr22:29282200-29287000	Weak transcription	Fetal Heart	heart
19	chr22:29282200-29287400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:29282200-29287600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:29282200-29287800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr22:29282200-29288000	Weak transcription	Right Ventricle	heart
23	chr22:29282200-29288200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr22:29282200-29290400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr22:29282200-29295000	Weak transcription	Brain Substantia Nigra	brain
26	chr22:29282400-29287600	Weak transcription	HMEC	breast
27	chr22:29282400-29287800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:29282400-29288000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:29282400-29290400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr22:29283000-29287600	Weak transcription	NHEK	skin
31	chr22:29283000-29287800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr22:29283000-29288000	Weak transcription	Esophagus	oesophagus
33	chr22:29283000-29288000	Weak transcription	Gastric	stomach
34	chr22:29283200-29288200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr22:29283400-29288000	Weak transcription	K562	blood
36	chr22:29283400-29294200	Weak transcription	Aorta	Aorta
37	chr22:29283400-29299000	Weak transcription	Fetal Stomach	stomach
38	chr22:29283600-29287000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29283600-29287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr22:29283600-29287400	Weak transcription	Small Intestine	intestine
41	chr22:29283800-29286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr22:29283800-29290200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr22:29284000-29287400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:29284000-29287800	Weak transcription	Fetal Intestine Small	intestine
45	chr22:29284200-29288200	Weak transcription	Colon Smooth Muscle	Colon
46	chr22:29284200-29290400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:29284200-29292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr22:29284400-29287200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr22:29284400-29287200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr22:29284400-29287400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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