Variant report

Variant	rs6732072
Chromosome Location	chr2:210914247-210914248
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:210910340..210914664-chr2:210915151..210918524,3	K562	blood:
2	chr2:210913785..210915896-chr2:210924611..210926176,2	MCF-7	breast:
3	chr2:210897940..210899527-chr2:210913482..210916323,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10179268	1.00[ASN][1000 genomes]
rs10192315	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]
rs1155845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11675027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11678206	1.00[ASN][1000 genomes]
rs11682370	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686587	1.00[ASN][1000 genomes]
rs11688180	1.00[ASN][1000 genomes]
rs11688922	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]
rs12989455	1.00[ASN][1000 genomes]
rs12992714	1.00[ASN][1000 genomes]
rs13006132	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13009890	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011543	1.00[ASN][1000 genomes]
rs13013030	1.00[CHB][hapmap]
rs13015354	1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017647	0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017752	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13020232	1.00[ASN][1000 genomes]
rs13021055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025700	1.00[ASN][1000 genomes]
rs13415601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1509568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs1509570	1.00[ASN][1000 genomes]
rs1509571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1509572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844058	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16844213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs2160020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs2539005	1.00[ASN][1000 genomes]
rs263668	1.00[ASN][1000 genomes]
rs263675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs263680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs263681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[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]
rs6435561	1.00[ASN][1000 genomes]
rs6714161	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716836	1.00[ASN][1000 genomes]
rs6732486	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6732506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735292	1.00[ASN][1000 genomes]
rs6754591	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760874	1.00[ASN][1000 genomes]
rs71350736	1.00[ASN][1000 genomes]
rs7557043	1.00[ASN][1000 genomes]
rs7609345	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv1802749	chr2:210905194-211255611	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6732072	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210868000-210920000	Weak transcription	Spleen	Spleen
2	chr2:210874000-210920800	Weak transcription	Fetal Heart	heart
3	chr2:210881800-210953000	Weak transcription	Gastric	stomach
4	chr2:210882400-210914600	Weak transcription	Small Intestine	intestine
5	chr2:210882400-210919400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:210882400-210922800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:210882400-210927800	Weak transcription	Right Ventricle	heart
8	chr2:210883000-210920600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:210885200-210914400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:210887800-210919600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:210889000-210919400	Weak transcription	HSMMtube	muscle
12	chr2:210889000-210920200	Weak transcription	Fetal Brain Male	brain
13	chr2:210889000-210925600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:210890000-210919200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:210891000-210915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:210891000-210927800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:210891400-210918800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:210893400-210939000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:210894000-210969400	Weak transcription	Fetal Kidney	kidney
20	chr2:210897000-210917000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:210899600-210919200	Weak transcription	Brain Anterior Caudate	brain
22	chr2:210902400-210919200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:210904200-210919400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:210905200-210914600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:210905600-210917400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:210905800-210914400	Weak transcription	HSMM	muscle
27	chr2:210907200-210919200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:210908200-210914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:210908600-210917400	Weak transcription	Liver	Liver
30	chr2:210908800-210914600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:210908800-210919200	Weak transcription	Adipose Nuclei	Adipose
32	chr2:210911600-210917800	Weak transcription	Fetal Thymus	thymus
33	chr2:210911600-210925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:210911600-210928000	Weak transcription	Primary T cells from cord blood	blood
35	chr2:210911600-210980800	Weak transcription	Pancreas	Pancrea
36	chr2:210911800-210914600	Weak transcription	Psoas Muscle	Psoas
37	chr2:210911800-210917400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:210911800-210917600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:210911800-210918200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:210911800-210919000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:210911800-210919200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:210911800-210919400	Weak transcription	Fetal Stomach	stomach
43	chr2:210911800-210919600	Weak transcription	Ovary	ovary
44	chr2:210911800-210920000	Weak transcription	Aorta	Aorta
45	chr2:210911800-210920600	Weak transcription	Esophagus	oesophagus
46	chr2:210911800-210920600	Weak transcription	Lung	lung
47	chr2:210911800-210921000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:210912000-210919200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:210912000-210919800	Weak transcription	Left Ventricle	heart
50	chr2:210912000-210920000	Weak transcription	Thymus	Thymus

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