Variant report

Variant	rs132531
Chromosome Location	chr22:29297365-29297366
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	chr22:29296014..29298873-chr22:29469784..29471423,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1065497	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12165962	0.82[CEU][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap]
rs1318025	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318026	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs132528	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs132529	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs132533	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132536	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs132543	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132548	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015500	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2064261	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2097461	0.89[JPT][hapmap]
rs2213645	0.95[JPT][hapmap]
rs2239815	1.00[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap]
rs2239828	0.96[CEU][hapmap]
rs2269577	0.89[JPT][hapmap]
rs2347447	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs3788409	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs469990	0.96[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469991	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs469992	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4822998	0.94[JPT][hapmap]
rs5752809	0.89[JPT][hapmap]
rs5752812	0.89[JPT][hapmap]
rs5752826	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762784	0.89[JPT][hapmap]
rs5762788	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs5762795	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs5762870	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762874	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762877	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5762880	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762881	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762882	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]
rs5762936	0.95[JPT][hapmap]
rs5997408	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5997412	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap]
rs6005915	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6005936	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6519766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715531	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287806	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7287918	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs763073	1.00[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.94[YRI][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8142067	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9625619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs132531	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs132531	ZNRF3	cis	parietal	SCAN
rs132531	XBP1	cis	cerebellum	SCAN
rs132531	MN1	cis	cerebellum	SCAN
rs132531	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29283400-29299000	Weak transcription	Fetal Stomach	stomach
2	chr22:29286000-29299000	Weak transcription	Ovary	ovary
3	chr22:29286800-29297800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29288000-29301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr22:29288400-29299000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:29288400-29299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr22:29288600-29298600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:29290800-29298400	Weak transcription	Fetal Muscle Leg	muscle
9	chr22:29290800-29298600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr22:29290800-29299000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr22:29291200-29300600	Weak transcription	Psoas Muscle	Psoas
12	chr22:29291400-29298400	Weak transcription	Fetal Intestine Large	intestine
13	chr22:29292000-29299000	Weak transcription	Right Atrium	heart
14	chr22:29292400-29297600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr22:29292400-29297600	Enhancers	HMEC	breast
16	chr22:29292400-29300600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:29292800-29299000	Weak transcription	Brain Germinal Matrix	brain
18	chr22:29293000-29299800	Weak transcription	A549	lung
19	chr22:29293200-29298400	Weak transcription	Right Ventricle	heart
20	chr22:29293200-29299000	Weak transcription	Left Ventricle	heart
21	chr22:29293400-29298600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:29293400-29298600	Weak transcription	Placenta	Placenta
23	chr22:29293400-29299000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr22:29293600-29299000	Weak transcription	Fetal Brain Male	brain
25	chr22:29293800-29298400	Weak transcription	Liver	Liver
26	chr22:29293800-29299000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr22:29293800-29299000	Weak transcription	Lung	lung
28	chr22:29293800-29299000	Weak transcription	Pancreas	Pancrea
29	chr22:29294600-29298800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:29295000-29298400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:29295200-29298800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr22:29295400-29298800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:29295400-29299000	Weak transcription	Spleen	Spleen
34	chr22:29295400-29299200	Weak transcription	Small Intestine	intestine
35	chr22:29295600-29297400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr22:29295600-29298600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:29295600-29298600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr22:29295600-29298600	Weak transcription	Fetal Kidney	kidney
39	chr22:29295600-29298800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:29295600-29298800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr22:29295600-29299000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr22:29295600-29299800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr22:29295600-29299800	Weak transcription	NHDF-Ad	bronchial
44	chr22:29295600-29300600	Weak transcription	Brain Substantia Nigra	brain
45	chr22:29295800-29297600	Enhancers	NHEK	skin
46	chr22:29295800-29300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:29296000-29297400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr22:29296000-29297400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr22:29296000-29299000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:29296000-29299200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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