Variant report

Variant	rs17039554
Chromosome Location	chr2:54714553-54714554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10171331	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10205013	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12477221	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045917	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087854	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233950	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4561702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635562	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671218	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671940	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671943	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58779052	0.92[ASN][1000 genomes]
rs6545409	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718276	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6754429	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72618660	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72618661	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72618662	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7599380	0.97[AMR][1000 genomes];0.97[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	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17039554	PSME4	cis	cerebellum	SCAN
rs17039554	VRK2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
2	chr2:54707600-54717600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:54707800-54720800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:54710600-54725000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:54710800-54715400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54710800-54715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:54710800-54715400	Weak transcription	K562	blood
8	chr2:54710800-54729600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:54711200-54715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54711200-54718800	Weak transcription	Aorta	Aorta
11	chr2:54711600-54715400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:54711600-54715400	Weak transcription	Fetal Brain Female	brain
13	chr2:54711600-54724400	Weak transcription	HSMMtube	muscle
14	chr2:54711600-54726000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:54711800-54714600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54711800-54715200	Weak transcription	Fetal Brain Male	brain
17	chr2:54711800-54715200	Weak transcription	Spleen	Spleen
18	chr2:54711800-54715200	Weak transcription	HepG2	liver
19	chr2:54711800-54715200	Weak transcription	NH-A	brain
20	chr2:54711800-54715200	Weak transcription	Osteobl	bone
21	chr2:54711800-54715400	Weak transcription	Small Intestine	intestine
22	chr2:54711800-54717800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:54711800-54721000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:54711800-54726200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:54712000-54714800	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:54712000-54715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:54712000-54715200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:54712000-54715200	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:54712000-54715200	Weak transcription	Psoas Muscle	Psoas
30	chr2:54712000-54715200	Weak transcription	Right Ventricle	heart
31	chr2:54712000-54715400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:54712000-54715400	Weak transcription	Fetal Stomach	stomach
33	chr2:54712000-54715400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:54712000-54715400	Weak transcription	Right Atrium	heart
35	chr2:54712000-54717800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:54712000-54717800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:54712000-54721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:54712200-54715400	Weak transcription	Brain Angular Gyrus	brain
39	chr2:54712200-54715400	Weak transcription	Brain Anterior Caudate	brain
40	chr2:54712200-54715400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:54712400-54715400	Weak transcription	Brain Substantia Nigra	brain
42	chr2:54712400-54717800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:54712400-54719600	Weak transcription	Lung	lung
44	chr2:54712400-54727800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:54712400-54729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:54712400-54737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:54712600-54715200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:54712600-54716200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:54712600-54727800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:54713800-54717000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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