Variant report

Variant	rs733164
Chromosome Location	chr22:27816784-27816785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4820756	0.93[ASN][1000 genomes]
rs4822875	0.85[AFR][1000 genomes]
rs5752540	0.80[AFR][1000 genomes]
rs738505	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv834167	chr22:27758395-27910985	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv459864	chr22:27760086-27865344	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv588875	chr22:27760086-27865344	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs733164	ST6GALNAC3	trans	cerebellum	SCAN
rs733164	EMID1	cis	cerebellum	SCAN
rs733164	SUSD2	cis	cerebellum	SCAN
rs733164	ZNF280B	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27812600-27816800	Enhancers	HUVEC	blood vessel
2	chr22:27812600-27817000	Enhancers	NH-A	brain
3	chr22:27812600-27817800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:27812800-27817400	Weak transcription	Fetal Thymus	thymus
5	chr22:27813800-27816800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr22:27813800-27817200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr22:27813800-27817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:27813800-27817600	Enhancers	Brain Germinal Matrix	brain
9	chr22:27814000-27816800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:27814000-27817000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:27814200-27816800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:27814200-27817800	Enhancers	Pancreas	Pancrea
13	chr22:27814400-27816800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:27814600-27817600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr22:27814800-27816800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:27814800-27816800	Enhancers	HMEC	breast
17	chr22:27814800-27817400	Enhancers	Brain Hippocampus Middle	brain
18	chr22:27814800-27817400	Enhancers	Brain Substantia Nigra	brain
19	chr22:27815200-27816800	Enhancers	HSMM	muscle
20	chr22:27815200-27817000	Enhancers	Brain Angular Gyrus	brain
21	chr22:27815200-27817400	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr22:27815400-27817200	Enhancers	Brain Cingulate Gyrus	brain
23	chr22:27815400-27817400	Enhancers	Liver	Liver
24	chr22:27815600-27816800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr22:27815600-27817400	Enhancers	Brain Anterior Caudate	brain
26	chr22:27815600-27817600	Enhancers	Fetal Kidney	kidney
27	chr22:27815600-27818000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr22:27816200-27816800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr22:27816200-27817600	Enhancers	Right Atrium	heart
30	chr22:27816200-27817800	Enhancers	Fetal Muscle Trunk	muscle
31	chr22:27816200-27817800	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr22:27816400-27816800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:27816400-27816800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr22:27816400-27816800	Enhancers	Ovary	ovary
35	chr22:27816400-27816800	Enhancers	A549	lung
36	chr22:27816400-27816800	Enhancers	NHDF-Ad	bronchial
37	chr22:27816400-27816800	Enhancers	NHLF	lung
38	chr22:27816400-27817000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr22:27816400-27817000	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr22:27816400-27817200	Enhancers	Aorta	Aorta
41	chr22:27816400-27817200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr22:27816400-27817200	Enhancers	Fetal Brain Male	brain
43	chr22:27816400-27817400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr22:27816400-27817400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr22:27816400-27817400	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr22:27816400-27817400	Enhancers	Hela-S3	cervix
47	chr22:27816400-27817600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr22:27816400-27817600	Enhancers	Adipose Nuclei	Adipose
49	chr22:27816400-27817600	Enhancers	Colon Smooth Muscle	Colon
50	chr22:27816400-27817600	Enhancers	Gastric	stomach

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