Variant report

Variant	rs5762942
Chromosome Location	chr22:29390049-29390050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2064084	0.84[MKK][hapmap]
rs2347788	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4823003	0.95[MKK][hapmap]
rs5762925	0.82[CHD][hapmap];0.81[GIH][hapmap]
rs5762936	1.00[CEU][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7290304	0.95[MKK][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5762942	MN1	cis	cerebellum	SCAN
rs5762942	GAL3ST1	cis	cerebellum	SCAN
rs5762942	ZNRF3	cis	parietal	SCAN
rs5762942	GGT5	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29365800-29394800	Weak transcription	Pancreas	Pancrea
2	chr22:29373400-29390800	Weak transcription	Hela-S3	cervix
3	chr22:29373600-29400200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr22:29374400-29395200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:29374600-29395600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr22:29374600-29400000	Weak transcription	Right Ventricle	heart
7	chr22:29374600-29401200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr22:29375600-29390800	Weak transcription	NHDF-Ad	bronchial
9	chr22:29375800-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29379600-29400800	Weak transcription	Fetal Brain Female	brain
11	chr22:29380800-29400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr22:29381000-29393000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:29381000-29395600	Weak transcription	Esophagus	oesophagus
14	chr22:29381200-29400400	Weak transcription	Lung	lung
15	chr22:29381600-29395400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr22:29381800-29390600	Weak transcription	Colonic Mucosa	Colon
17	chr22:29382000-29400200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr22:29382400-29393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:29383400-29400200	Weak transcription	Right Atrium	heart
20	chr22:29383600-29400400	Weak transcription	Aorta	Aorta
21	chr22:29383800-29395400	Weak transcription	NHEK	skin
22	chr22:29383800-29399800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:29383800-29400000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr22:29384600-29395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr22:29385000-29395200	Weak transcription	Left Ventricle	heart
26	chr22:29385000-29395600	Weak transcription	A549	lung
27	chr22:29385600-29394600	Weak transcription	Fetal Kidney	kidney
28	chr22:29385600-29395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr22:29385600-29400800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr22:29385600-29401000	Weak transcription	Colon Smooth Muscle	Colon
31	chr22:29385800-29391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr22:29385800-29397800	Weak transcription	Fetal Lung	lung
33	chr22:29386000-29395600	Weak transcription	Osteobl	bone
34	chr22:29386200-29392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:29386200-29395400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:29386200-29395600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr22:29386200-29400000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr22:29386400-29395400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr22:29386400-29395800	Weak transcription	HMEC	breast
40	chr22:29386600-29390200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr22:29386600-29395400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:29386800-29390200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr22:29386800-29395600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr22:29387000-29395400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr22:29388600-29400400	Weak transcription	Placenta	Placenta
46	chr22:29388800-29399200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr22:29388800-29400200	Weak transcription	Brain Germinal Matrix	brain
48	chr22:29388800-29400800	Weak transcription	Gastric	stomach
49	chr22:29389000-29392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:29389000-29394800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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