Variant report

Variant	rs13006132
Chromosome Location	chr2:210879917-210879918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:210869956..210875307-chr2:210879212..210883856,7	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

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];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];1.00[ASN][1000 genomes]
rs11682370	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989455	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992714	1.00[ASN][1000 genomes]
rs13009071	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs13009890	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];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017647	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018349	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];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];0.84[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]
rs16844213	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs2160020	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][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];0.84[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[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[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
rs13006132	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	chr2:210868200-210880000	Weak transcription	Aorta	Aorta
3	chr2:210868200-210880000	Weak transcription	Esophagus	oesophagus
4	chr2:210868200-210883200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:210868400-210880600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:210868400-210899000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:210869000-210881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:210869200-210880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:210869200-210880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:210869200-210880600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:210869400-210880000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:210869400-210880800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:210869400-210883000	Weak transcription	Colonic Mucosa	Colon
14	chr2:210869400-210891400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:210870000-210880000	Weak transcription	Gastric	stomach
16	chr2:210870000-210886000	Weak transcription	Fetal Brain Male	brain
17	chr2:210870600-210880000	Weak transcription	Pancreas	Pancrea
18	chr2:210870800-210890000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:210871000-210889400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:210871000-210893800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:210871200-210889200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:210871200-210893000	Strong transcription	Dnd41	blood
23	chr2:210871200-210893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:210871200-210911400	Weak transcription	Psoas Muscle	Psoas
25	chr2:210871600-210880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:210871600-210891800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:210871800-210881200	Weak transcription	Small Intestine	intestine
28	chr2:210871800-210890600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:210872400-210884200	Strong transcription	A549	lung
30	chr2:210872400-210890000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:210872400-210893800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:210872600-210891400	Strong transcription	Fetal Thymus	thymus
33	chr2:210872600-210907600	Weak transcription	Stomach Mucosa	stomach
34	chr2:210872800-210880400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:210872800-210889200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:210872800-210890800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:210872800-210894200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:210873000-210881200	Weak transcription	Right Ventricle	heart
39	chr2:210873000-210890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:210873000-210893800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:210873200-210889400	Strong transcription	Fetal Lung	lung
42	chr2:210873400-210880000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:210873400-210891600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:210873600-210881200	Weak transcription	Thymus	Thymus
45	chr2:210873600-210891400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:210873800-210880200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:210873800-210889000	Strong transcription	Primary B cells from cord blood	blood
48	chr2:210874000-210890000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:210874000-210920800	Weak transcription	Fetal Heart	heart
50	chr2:210874200-210893800	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links