Variant report

Variant	rs12167141
Chromosome Location	chr22:31273284-31273285
allele	A/T
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	MXI1	chr22:31272554-31273709	SK-N-SH	brain:	n/a	chr22:31272570-31272579
2	NFIC	chr22:31272788-31273444	ECC-1	luminal epithelium:	n/a	n/a
3	EBF1	chr22:31273113-31273479	GM12878	blood:	n/a	n/a
4	MAX	chr22:31272899-31273535	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr22:31272833-31273700	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr22:31272791-31273574	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr22:31272846-31273685	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31264858..31267090-chr22:31269801..31273522,3	K562	blood:
2	chr22:31268537..31270740-chr22:31271570..31273370,2	K562	blood:

Variant related genes	Relation type
OSBP2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11089481	0.81[CEU][hapmap];0.83[CHB][hapmap];0.88[TSI][hapmap]
rs2240175	0.86[TSI][hapmap]
rs2240176	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes]
rs2240177	0.86[TSI][hapmap]
rs2240180	0.86[TSI][hapmap]
rs3747151	0.85[TSI][hapmap]
rs3827330	0.90[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs4820921	0.90[CEU][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs5753373	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs5753377	0.83[ASN][1000 genomes]
rs5753394	0.86[TSI][hapmap]
rs5997802	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7284767	0.80[TSI][hapmap]
rs7291471	0.80[EUR][1000 genomes]
rs737927	0.85[TSI][hapmap]
rs8004	0.86[TSI][hapmap]
rs8139350	0.90[CEU][hapmap]
rs8140448	0.85[CEU][hapmap];0.88[TSI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12167141	MORC2-AS1	cis	Nerve Tibial	GTEx
rs12167141	MORC2-AS1	cis	Thyroid	GTEx
rs12167141	MORC2-AS1	cis	Whole Blood	GTEx
rs12167141	MORC2	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31265200-31299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:31265800-31274000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr22:31266400-31295200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr22:31268800-31273600	Weak transcription	Fetal Intestine Small	intestine
5	chr22:31268800-31277200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:31269000-31276800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:31269200-31277400	Weak transcription	Gastric	stomach
8	chr22:31269400-31284200	Weak transcription	NHEK	skin
9	chr22:31269800-31273600	Weak transcription	Spleen	Spleen
10	chr22:31269800-31277800	Weak transcription	Pancreas	Pancrea
11	chr22:31269800-31283400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr22:31270800-31275800	Enhancers	Brain Hippocampus Middle	brain
13	chr22:31270800-31278400	Enhancers	Fetal Muscle Leg	muscle
14	chr22:31271000-31275800	Weak transcription	Hela-S3	cervix
15	chr22:31271200-31273800	Enhancers	Fetal Muscle Trunk	muscle
16	chr22:31271200-31274400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr22:31271200-31276400	Enhancers	Left Ventricle	heart
18	chr22:31271600-31275800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr22:31271600-31275800	Enhancers	Right Atrium	heart
20	chr22:31271600-31276400	Enhancers	Brain Cingulate Gyrus	brain
21	chr22:31271600-31277800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr22:31271800-31273400	Enhancers	Brain Germinal Matrix	brain
23	chr22:31271800-31276000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr22:31271800-31276400	Enhancers	Brain Substantia Nigra	brain
25	chr22:31271800-31276600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr22:31272000-31275800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr22:31272000-31277400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr22:31272000-31278400	Enhancers	Right Ventricle	heart
29	chr22:31272200-31275800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:31272200-31275800	Enhancers	HSMM	muscle
31	chr22:31272200-31276000	Enhancers	Brain Angular Gyrus	brain
32	chr22:31272200-31277600	Enhancers	Placenta	Placenta
33	chr22:31272200-31277800	Enhancers	Fetal Lung	lung
34	chr22:31272200-31280600	Enhancers	Fetal Heart	heart
35	chr22:31272400-31273800	Enhancers	Fetal Stomach	stomach
36	chr22:31272400-31273800	Weak transcription	HSMMtube	muscle
37	chr22:31272600-31274200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr22:31272600-31275800	Enhancers	NHDF-Ad	bronchial
39	chr22:31272800-31274400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:31272800-31274400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr22:31273000-31273600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr22:31273000-31275400	Enhancers	Brain Anterior Caudate	brain
43	chr22:31273000-31275400	Enhancers	Fetal Brain Female	brain
44	chr22:31273000-31277800	Enhancers	Fetal Brain Male	brain
45	chr22:31273200-31277000	Weak transcription	A549	lung
46	chr22:31273200-31277800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links