Variant report

Variant	rs10192315
Chromosome Location	chr2:210875407-210875408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10179268	1.00[ASN][1000 genomes]
rs1155845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11675027	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11682370	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688922	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]
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];1.00[ASN][1000 genomes]
rs13009890	0.92[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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018349	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13021055	1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415601	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]
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];0.86[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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716836	1.00[ASN][1000 genomes]
rs6732072	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732486	1.00[ASN][1000 genomes]
rs6732506	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754591	1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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
rs10192315	PLEKHM3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210868000-210920000	Weak transcription	Spleen	Spleen
2	chr2:210868200-210879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:210868200-210880000	Weak transcription	Aorta	Aorta
4	chr2:210868200-210880000	Weak transcription	Esophagus	oesophagus
5	chr2:210868200-210883200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:210868400-210876000	Weak transcription	Placenta	Placenta
7	chr2:210868400-210879800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:210868400-210880600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:210868400-210899000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:210869000-210881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:210869200-210875800	Weak transcription	NHLF	lung
12	chr2:210869200-210878400	Weak transcription	Osteobl	bone
13	chr2:210869200-210879600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:210869200-210879600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:210869200-210880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:210869200-210880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:210869200-210880600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:210869400-210879800	Weak transcription	HSMMtube	muscle
19	chr2:210869400-210880000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:210869400-210880800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:210869400-210883000	Weak transcription	Colonic Mucosa	Colon
22	chr2:210869400-210891400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:210869600-210879800	Weak transcription	Fetal Kidney	kidney
24	chr2:210870000-210880000	Weak transcription	Gastric	stomach
25	chr2:210870000-210886000	Weak transcription	Fetal Brain Male	brain
26	chr2:210870600-210875800	Weak transcription	Fetal Brain Female	brain
27	chr2:210870600-210877000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:210870600-210877200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:210870600-210877200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:210870600-210877200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:210870600-210877200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:210870600-210879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:210870600-210880000	Weak transcription	Pancreas	Pancrea
34	chr2:210870800-210876000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:210870800-210890000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:210871000-210889400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:210871000-210893800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:210871200-210877000	Weak transcription	Brain Angular Gyrus	brain
39	chr2:210871200-210879800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:210871200-210889200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:210871200-210893000	Strong transcription	Dnd41	blood
42	chr2:210871200-210893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:210871200-210911400	Weak transcription	Psoas Muscle	Psoas
44	chr2:210871400-210878200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:210871600-210876800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:210871600-210877000	Weak transcription	Brain Hippocampus Middle	brain
47	chr2:210871600-210879600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:210871600-210880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:210871600-210891800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:210871800-210876200	Strong transcription	Primary T cells from cord blood	blood

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