Variant report

Variant	rs7593466
Chromosome Location	chr2:209099479-209099480
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:209099425-209100503	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:209099467-209120161	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000263524	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10932255	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11883490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12478635	0.82[CHB][hapmap]
rs16840769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16840781	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4290589	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56935816	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67739507	0.92[ASN][1000 genomes]
rs67816904	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525747	chr2:209087335-209116753	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7593466	PLEKHM3	cis	cerebellum	SCAN
rs7593466	ACADL	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209087400-209100000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:209087600-209103400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:209090000-209099800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:209090000-209103000	Weak transcription	Osteobl	bone
5	chr2:209090000-209104400	Weak transcription	NHEK	skin
6	chr2:209090200-209100600	Weak transcription	HMEC	breast
7	chr2:209091000-209102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:209093000-209118400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:209095200-209101600	Weak transcription	HepG2	liver
10	chr2:209095400-209101800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:209096200-209104400	Weak transcription	HSMM	muscle
12	chr2:209097000-209100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:209097200-209099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:209097200-209099800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:209097200-209100000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:209097200-209100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:209097200-209100000	Weak transcription	Fetal Kidney	kidney
18	chr2:209097200-209100200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:209097200-209100200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:209097200-209101400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:209097200-209101800	Weak transcription	Fetal Lung	lung
22	chr2:209097200-209102000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:209097200-209102000	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:209097400-209099600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:209097400-209100000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:209097400-209100800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:209097400-209104600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:209097600-209100200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:209097600-209100600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:209097600-209101800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:209097800-209099600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:209097800-209100000	Weak transcription	Aorta	Aorta
33	chr2:209097800-209100200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:209097800-209100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:209097800-209101400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:209097800-209103000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:209097800-209103800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:209097800-209104400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:209098000-209099600	Weak transcription	Primary T cells from cord blood	blood
40	chr2:209098000-209099800	Weak transcription	Adipose Nuclei	Adipose
41	chr2:209098000-209100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:209098000-209100000	Weak transcription	Fetal Intestine Small	intestine
43	chr2:209098000-209100400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:209098200-209099800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:209098200-209099800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:209098200-209099800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:209098200-209099800	Weak transcription	Fetal Brain Female	brain
48	chr2:209098200-209099800	Weak transcription	Gastric	stomach
49	chr2:209098200-209099800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:209098200-209100000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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