Variant report

Variant	rs6005427
Chromosome Location	chr22:27817300-27817301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs136944	0.80[ASN][1000 genomes]
rs136945	0.85[ASN][1000 genomes]
rs136948	0.85[ASN][1000 genomes]
rs136949	0.85[ASN][1000 genomes]
rs136955	0.90[ASN][1000 genomes]
rs136956	0.92[ASN][1000 genomes]
rs136961	0.95[ASN][1000 genomes]
rs1884127	0.87[ASN][1000 genomes]
rs1884128	0.87[ASN][1000 genomes]
rs1884129	0.87[ASN][1000 genomes]
rs34716864	0.87[ASN][1000 genomes]
rs4822876	0.87[ASN][1000 genomes]
rs5752544	0.87[ASN][1000 genomes]
rs5762139	0.87[ASN][1000 genomes]
rs6005422	0.85[ASN][1000 genomes]
rs6005423	0.92[ASN][1000 genomes]
rs6005425	0.95[ASN][1000 genomes]
rs73427534	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs79557	0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6005427	HPS4,LOC100128401	cis	cerebellar cortex	BrainEAC

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27812600-27817800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr22:27812800-27817400	Weak transcription	Fetal Thymus	thymus
3	chr22:27813800-27817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:27813800-27817600	Enhancers	Brain Germinal Matrix	brain
5	chr22:27814200-27817800	Enhancers	Pancreas	Pancrea
6	chr22:27814600-27817600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:27814800-27817400	Enhancers	Brain Hippocampus Middle	brain
8	chr22:27814800-27817400	Enhancers	Brain Substantia Nigra	brain
9	chr22:27815200-27817400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr22:27815400-27817400	Enhancers	Liver	Liver
11	chr22:27815600-27817400	Enhancers	Brain Anterior Caudate	brain
12	chr22:27815600-27817600	Enhancers	Fetal Kidney	kidney
13	chr22:27815600-27818000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr22:27816200-27817600	Enhancers	Right Atrium	heart
15	chr22:27816200-27817800	Enhancers	Fetal Muscle Trunk	muscle
16	chr22:27816200-27817800	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr22:27816400-27817400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr22:27816400-27817400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr22:27816400-27817400	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr22:27816400-27817400	Enhancers	Hela-S3	cervix
21	chr22:27816400-27817600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr22:27816400-27817600	Enhancers	Adipose Nuclei	Adipose
23	chr22:27816400-27817600	Enhancers	Colon Smooth Muscle	Colon
24	chr22:27816400-27817600	Enhancers	Gastric	stomach
25	chr22:27816400-27817600	Enhancers	Left Ventricle	heart
26	chr22:27816400-27817600	Flanking Active TSS	Osteobl	bone
27	chr22:27816400-27817800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:27816400-27817800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:27816400-27817800	Enhancers	Fetal Lung	lung
30	chr22:27816600-27817400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr22:27816600-27817400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr22:27816600-27817400	Enhancers	Psoas Muscle	Psoas
33	chr22:27816600-27817400	Flanking Active TSS	NHEK	skin
34	chr22:27816600-27817600	Enhancers	Colonic Mucosa	Colon
35	chr22:27816600-27817600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr22:27816600-27817600	Bivalent Enhancer	Fetal Stomach	stomach
37	chr22:27816600-27817600	Enhancers	Right Ventricle	heart
38	chr22:27816600-27817800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:27816800-27817400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr22:27816800-27817400	Flanking Active TSS	NHDF-Ad	bronchial
41	chr22:27816800-27817400	Flanking Active TSS	NHLF	lung
42	chr22:27816800-27817600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:27816800-27817600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:27816800-27817600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:27816800-27817600	Enhancers	Lung	lung
46	chr22:27816800-27817600	Flanking Active TSS	HUVEC	blood vessel
47	chr22:27817000-27817400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr22:27817000-27817400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr22:27817000-27817400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:27817000-27817600	Enhancers	Esophagus	oesophagus

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