Variant report

Variant	rs11688922
Chromosome Location	chr2:210899032-210899033
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:210898222..210900369-chr2:210901306..210904238,3	MCF-7	breast:
2	chr2:210893344..210897123-chr2:210897733..210899540,3	K562	blood:
3	chr2:210897940..210899527-chr2:210913482..210916323,2	K562	blood:
4	chr2:210897973..210901290-chr2:210902919..210906979,4	K562	blood:
5	chr2:210890930..210893615-chr2:210897966..210899607,2	MCF-7	breast:
6	chr2:210896066..210901290-chr2:210902199..210908006,8	K562	blood:
7	chr2:210898830..210901084-chr2:210903184..210905087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229127	Chromatin interaction
ENSG00000272807	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10179268	1.00[ASN][1000 genomes]
rs10192315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11675027	1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs11682370	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989455	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992714	1.00[ASN][1000 genomes]
rs13006132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009071	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs13009890	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011543	1.00[ASN][1000 genomes]
rs13013030	1.00[CHB][hapmap]
rs13015354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017647	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018349	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13020232	1.00[ASN][1000 genomes]
rs13021055	1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025700	1.00[ASN][1000 genomes]
rs13415601	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1509568	1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs1509570	1.00[ASN][1000 genomes]
rs1509571	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1509572	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844058	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844213	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs2160020	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs2539005	1.00[ASN][1000 genomes]
rs263668	1.00[ASN][1000 genomes]
rs263675	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs263680	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs263681	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs263686	1.00[ASN][1000 genomes]
rs34334556	1.00[ASN][1000 genomes]
rs34678259	1.00[ASN][1000 genomes]
rs35125543	1.00[ASN][1000 genomes]
rs62202972	1.00[ASN][1000 genomes]
rs6714161	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716836	1.00[ASN][1000 genomes]
rs6732072	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732486	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6732506	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735292	1.00[ASN][1000 genomes]
rs6754591	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760874	1.00[ASN][1000 genomes]
rs71350736	1.00[ASN][1000 genomes]
rs7609345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431969	chr2:210682494-211074494	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1004426	chr2:210709999-211001680	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv1795338	chr2:210758078-211098113	Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11688922	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210868000-210920000	Weak transcription	Spleen	Spleen
2	chr2:210871200-210911400	Weak transcription	Psoas Muscle	Psoas
3	chr2:210872600-210907600	Weak transcription	Stomach Mucosa	stomach
4	chr2:210874000-210920800	Weak transcription	Fetal Heart	heart
5	chr2:210881800-210953000	Weak transcription	Gastric	stomach
6	chr2:210882400-210911400	Weak transcription	Esophagus	oesophagus
7	chr2:210882400-210914600	Weak transcription	Small Intestine	intestine
8	chr2:210882400-210919400	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:210882400-210922800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:210882400-210927800	Weak transcription	Right Ventricle	heart
11	chr2:210882800-210911400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:210883000-210920600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:210883400-210911200	Weak transcription	Aorta	Aorta
14	chr2:210883400-210911200	Weak transcription	Pancreas	Pancrea
15	chr2:210883600-210911400	Weak transcription	Lung	lung
16	chr2:210884600-210911000	Weak transcription	Ovary	ovary
17	chr2:210884600-210912600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:210885200-210914400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:210887800-210919600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:210888000-210913400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:210888200-210905400	Weak transcription	Fetal Brain Female	brain
22	chr2:210889000-210905400	Weak transcription	NHDF-Ad	bronchial
23	chr2:210889000-210909200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:210889000-210911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:210889000-210911400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:210889000-210912200	Weak transcription	HMEC	breast
27	chr2:210889000-210919400	Weak transcription	HSMMtube	muscle
28	chr2:210889000-210920200	Weak transcription	Fetal Brain Male	brain
29	chr2:210889000-210925600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:210889200-210902800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:210889200-210911400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:210889200-210911400	Weak transcription	Left Ventricle	heart
33	chr2:210889200-210911600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:210889200-210913400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:210889200-210913400	Weak transcription	NH-A	brain
36	chr2:210889400-210910600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:210889400-210911200	Weak transcription	Fetal Lung	lung
38	chr2:210890000-210919200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:210890200-210911200	Weak transcription	HUVEC	blood vessel
40	chr2:210890600-210901000	Weak transcription	Fetal Stomach	stomach
41	chr2:210890600-210908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:210890600-210911000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:210890600-210911200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:210890800-210912000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:210891000-210915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:210891000-210927800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:210891400-210910400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:210891400-210910600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:210891400-210911200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:210891400-210911200	Weak transcription	A549	lung

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