Variant report

Variant	rs5753369
Chromosome Location	chr22:31279536-31279537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31279205-31279580	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31275934..31283484-chr22:31284259..31290179,9	K562	blood:
2	chr22:31197932..31200632-chr22:31277556..31279814,2	K562	blood:
3	chr22:31278602..31281426-chr22:31284915..31287242,4	K562	blood:

Variant related genes	Relation type
OSBP2	TF binding region
ENSG00000184792	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1003480	0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap]
rs1005252	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs10854601	1.00[YRI][hapmap]
rs2074578	0.83[ASW][hapmap];0.94[CHB][hapmap];0.86[YRI][hapmap]
rs2240175	1.00[YRI][hapmap]
rs2240177	0.93[YRI][hapmap]
rs2240179	0.93[YRI][hapmap]
rs2240180	1.00[YRI][hapmap]
rs2240182	0.83[ASW][hapmap];0.88[CHB][hapmap];0.82[LWK][hapmap];0.93[YRI][hapmap]
rs2240183	0.93[YRI][hapmap]
rs2285918	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs3747151	0.93[YRI][hapmap]
rs3788426	0.93[YRI][hapmap]
rs3804085	0.90[YRI][hapmap]
rs4820916	0.93[YRI][hapmap]
rs5749186	1.00[CHB][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs5753394	1.00[YRI][hapmap]
rs5753398	0.83[CHB][hapmap];0.93[YRI][hapmap]
rs5753407	0.93[YRI][hapmap]
rs5753408	0.93[YRI][hapmap]
rs5753410	0.93[YRI][hapmap]
rs5997830	0.93[YRI][hapmap]
rs5997838	0.93[YRI][hapmap]
rs5997846	0.89[YRI][hapmap]
rs7284767	0.93[YRI][hapmap]
rs7291361	0.93[YRI][hapmap]
rs737924	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs739896	0.96[YRI][hapmap]
rs8004	0.83[ASW][hapmap]
rs8135974	0.93[YRI][hapmap]
rs9609183	0.87[YRI][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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv914974	chr22:31249333-31279536	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753369	SMTN	cis	cerebellum	SCAN
rs5753369	MORC2-AS1	cis	Thyroid	GTEx
rs5753369	MORC2	cis	brain	BrainEAC

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31265200-31299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:31266400-31295200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr22:31269400-31284200	Weak transcription	NHEK	skin
4	chr22:31269800-31283400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr22:31272200-31280600	Enhancers	Fetal Heart	heart
6	chr22:31274200-31308400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr22:31275200-31284200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:31275400-31280200	Weak transcription	Brain Anterior Caudate	brain
9	chr22:31275600-31283400	Weak transcription	Brain Germinal Matrix	brain
10	chr22:31275800-31283600	Weak transcription	HSMM	muscle
11	chr22:31275800-31284800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr22:31275800-31285000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr22:31275800-31289400	Weak transcription	NHDF-Ad	bronchial
14	chr22:31276400-31283400	Weak transcription	Fetal Brain Female	brain
15	chr22:31276400-31283600	Weak transcription	Brain Substantia Nigra	brain
16	chr22:31276600-31280200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:31277400-31280000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr22:31277800-31295200	Weak transcription	Fetal Brain Male	brain
19	chr22:31278000-31280200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
20	chr22:31278000-31280400	Weak transcription	Brain Angular Gyrus	brain
21	chr22:31278000-31283400	Weak transcription	Brain Hippocampus Middle	brain
22	chr22:31278000-31290000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr22:31278200-31280000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr22:31278200-31280800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr22:31278200-31283200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr22:31278200-31283400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:31278200-31284400	Weak transcription	Gastric	stomach
28	chr22:31278200-31285200	Weak transcription	Esophagus	oesophagus
29	chr22:31278200-31286600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:31278200-31288200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr22:31278400-31280000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr22:31278400-31280400	Weak transcription	Spleen	Spleen
33	chr22:31278400-31281800	Enhancers	Placenta	Placenta
34	chr22:31278400-31283400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr22:31278400-31283400	Weak transcription	Fetal Stomach	stomach
36	chr22:31278400-31283600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr22:31278400-31283600	Weak transcription	Pancreas	Pancrea
38	chr22:31278400-31286200	Weak transcription	Fetal Muscle Leg	muscle
39	chr22:31278400-31288600	Weak transcription	HSMMtube	muscle
40	chr22:31278400-31291800	Weak transcription	HMEC	breast
41	chr22:31278400-31292600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr22:31278400-31301600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr22:31278600-31279800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr22:31278600-31280600	Enhancers	Fetal Lung	lung
45	chr22:31278600-31285600	Weak transcription	Liver	Liver
46	chr22:31278600-31321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:31278800-31279600	Enhancers	HepG2	liver
48	chr22:31278800-31295000	Weak transcription	Small Intestine	intestine
49	chr22:31278800-31301600	Weak transcription	A549	lung
50	chr22:31279000-31279600	Enhancers	Duodenum Mucosa	Duodenum

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