Variant report

Variant	rs2240176
Chromosome Location	chr22:31321948-31321949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31318522..31320087-chr22:31320410..31322859,2	MCF-7	breast:
2	chr22:31319777..31322266-chr22:31479907..31481786,2	MCF-7	breast:
3	chr22:31321691..31323694-chr22:31328611..31331015,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OSBP2-1	chr22:31320716-31322537	ENSG00000235989.2
2	lnc-OSBP2-1	chr22:31320716-31323477	NONHSAT084818
3	lnc-OSBP2-1	chr22:31320716-31322641	ENSG00000235989.3

No data

Variant related genes	Relation type
ENSG00000133422	Chromatin interaction
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10854601	0.83[EUR][1000 genomes]
rs11089481	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11703597	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11705565	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12166294	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12167141	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]
rs12167144	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12168307	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1807686	0.83[EUR][1000 genomes]
rs2016654	0.81[EUR][1000 genomes]
rs2072132	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2240175	0.80[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2240177	0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2240180	0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2240181	0.93[EUR][1000 genomes]
rs2240183	0.83[EUR][1000 genomes]
rs3747151	0.84[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3788426	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs3804084	0.83[EUR][1000 genomes]
rs3804085	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs3827330	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3948685	0.81[EUR][1000 genomes]
rs4820916	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs4820921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749185	0.82[TSI][hapmap]
rs5749192	0.83[EUR][1000 genomes]
rs5753373	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753377	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753378	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753379	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753383	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5753386	0.82[EUR][1000 genomes]
rs5753394	0.85[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753396	0.80[AMR][1000 genomes]
rs5753408	0.83[EUR][1000 genomes]
rs5997802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997830	0.80[EUR][1000 genomes]
rs5997837	0.90[EUR][1000 genomes]
rs5997838	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs5997842	0.83[EUR][1000 genomes]
rs7284474	0.90[EUR][1000 genomes]
rs7284767	0.85[MEX][hapmap];0.86[TSI][hapmap]
rs7290078	0.80[AMR][1000 genomes]
rs7291361	0.83[EUR][1000 genomes]
rs7291471	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737924	0.84[TSI][hapmap]
rs737926	0.82[EUR][1000 genomes]
rs737927	0.84[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs739896	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8004	0.80[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs8139350	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8140448	0.95[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2240176	MORC2-AS1	cis	Nerve Tibial	GTEx
rs2240176	MORC2	cis	parietal	SCAN
rs2240176	TUG1	Cis_1M	lymphoblastoid	RTeQTL
rs2240176	MORC2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2240176	MORC2-AS1	cis	Whole Blood	GTEx
rs2240176	MORC2-AS1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31316800-31323000	Weak transcription	Hela-S3	cervix
2	chr22:31317600-31323000	Weak transcription	A549	lung
3	chr22:31317600-31324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:31317600-31364000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:31317800-31323200	Weak transcription	HMEC	breast
6	chr22:31318400-31322800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:31318400-31322800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr22:31318400-31324400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr22:31318400-31342200	Weak transcription	Right Atrium	heart
10	chr22:31318600-31322000	Weak transcription	Colonic Mucosa	Colon
11	chr22:31318600-31323000	Weak transcription	Colon Smooth Muscle	Colon
12	chr22:31318600-31323000	Weak transcription	Fetal Brain Male	brain
13	chr22:31318600-31323600	Weak transcription	Fetal Kidney	kidney
14	chr22:31318600-31328000	Weak transcription	Fetal Heart	heart
15	chr22:31318600-31329000	Weak transcription	Stomach Mucosa	stomach
16	chr22:31318800-31322000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr22:31318800-31322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr22:31318800-31322600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr22:31318800-31323000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr22:31318800-31323200	Weak transcription	GM12878-XiMat	blood
21	chr22:31318800-31324200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr22:31319000-31333200	Strong transcription	Primary T cells from cord blood	blood
23	chr22:31319000-31343600	Strong transcription	Fetal Stomach	stomach
24	chr22:31319200-31322600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr22:31319200-31324000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr22:31319200-31324800	Strong transcription	Fetal Brain Female	brain
27	chr22:31319200-31338600	Strong transcription	Thymus	Thymus
28	chr22:31319200-31344000	Strong transcription	Fetal Intestine Small	intestine
29	chr22:31319200-31345200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr22:31319200-31347400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:31319200-31350800	Strong transcription	Brain Germinal Matrix	brain
32	chr22:31319200-31351800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr22:31319400-31327600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:31319400-31336400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:31319400-31337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr22:31319400-31342200	Strong transcription	Fetal Muscle Leg	muscle
37	chr22:31319600-31326000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr22:31319600-31327000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr22:31319600-31342000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:31319600-31342200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:31319600-31343200	Strong transcription	Placenta	Placenta
42	chr22:31319600-31345200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr22:31319800-31342200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr22:31319800-31343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr22:31319800-31343200	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr22:31319800-31353200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr22:31319800-31355800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr22:31320000-31342000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr22:31320000-31342200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr22:31320000-31342400	Strong transcription	Brain Cingulate Gyrus	brain

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