Variant report

Variant	rs469990
Chromosome Location	chr22:29304200-29304201
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1065497	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12165962	0.84[JPT][hapmap]
rs1318025	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1318026	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132528	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs132529	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs132531	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]
rs132533	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs132543	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132548	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2015500	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064261	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2097461	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs2213645	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2239815	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs2239828	0.92[CEU][hapmap]
rs2269577	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs2347447	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs3788409	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs469991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469992	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4822998	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs5752809	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap]
rs5752812	0.82[CEU][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap]
rs5752826	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762784	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762788	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap]
rs5762795	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs5762870	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762874	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762877	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5762880	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762881	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762882	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]
rs5762936	0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs5997408	0.89[JPT][hapmap]
rs5997412	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap];0.81[MEX][hapmap]
rs6005915	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6005936	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6519766	0.96[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];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs715531	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7287806	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7287918	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763073	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs8136297	0.81[EUR][1000 genomes]
rs8137262	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8142067	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9620841	0.96[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];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625619	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs469990	MN1	cis	cerebellum	SCAN
rs469990	ZNRF3	cis	parietal	SCAN
rs469990	GAL3ST1	cis	cerebellum	SCAN
rs469990	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs469990	XBP1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29296800-29310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr22:29298400-29308400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr22:29298400-29310400	Enhancers	Fetal Intestine Large	intestine
4	chr22:29298600-29304600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr22:29298600-29305000	Enhancers	Brain Anterior Caudate	brain
6	chr22:29298600-29305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:29298800-29304400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr22:29298800-29305200	Enhancers	Brain Cingulate Gyrus	brain
9	chr22:29299000-29309200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr22:29299200-29304400	Weak transcription	Brain Germinal Matrix	brain
11	chr22:29299600-29307000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:29300000-29307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr22:29300800-29304400	Enhancers	Stomach Smooth Muscle	stomach
14	chr22:29300800-29307000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr22:29300800-29307400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr22:29300800-29307600	Weak transcription	Small Intestine	intestine
17	chr22:29301000-29304200	Weak transcription	NHEK	skin
18	chr22:29301000-29304600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr22:29301000-29304600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr22:29301000-29304800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr22:29301000-29305400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:29301000-29305400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:29301000-29306800	Weak transcription	NHLF	lung
24	chr22:29301200-29304200	Weak transcription	Fetal Muscle Leg	muscle
25	chr22:29301200-29306400	Weak transcription	Fetal Heart	heart
26	chr22:29301200-29306600	Weak transcription	Adipose Nuclei	Adipose
27	chr22:29301400-29306600	Weak transcription	Fetal Stomach	stomach
28	chr22:29301400-29306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr22:29301400-29306800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr22:29301600-29304400	Enhancers	Brain Hippocampus Middle	brain
31	chr22:29301800-29304600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:29301800-29304800	Weak transcription	Esophagus	oesophagus
33	chr22:29301800-29306600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:29301800-29307200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:29302000-29307400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:29302400-29304400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr22:29302400-29304600	Genic enhancers	HepG2	liver
38	chr22:29302400-29304800	Enhancers	Brain Angular Gyrus	brain
39	chr22:29302400-29304800	Weak transcription	Lung	lung
40	chr22:29302400-29305800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr22:29302400-29306400	Weak transcription	Placenta	Placenta
42	chr22:29302400-29306400	Weak transcription	Hela-S3	cervix
43	chr22:29302400-29307000	Weak transcription	Psoas Muscle	Psoas
44	chr22:29302600-29306400	Weak transcription	Fetal Lung	lung
45	chr22:29302600-29306600	Weak transcription	Right Atrium	heart
46	chr22:29302800-29304400	Weak transcription	Liver	Liver
47	chr22:29302800-29306400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr22:29302800-29306800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr22:29303200-29304400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr22:29303200-29304800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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