Variant report

Variant	rs6545409
Chromosome Location	chr2:54709683-54709684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10171331	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12477221	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17039554	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045917	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087854	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35001659	0.88[EUR][1000 genomes]
rs4233950	0.83[EUR][1000 genomes]
rs4561702	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4635562	0.81[EUR][1000 genomes]
rs4671218	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671933	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671935	0.85[EUR][1000 genomes]
rs4671940	0.93[ASN][1000 genomes]
rs4671943	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58779052	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6718276	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6754429	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72618659	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72618660	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72618661	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72618662	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599380	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[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	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6545409	VRK2	cis	cerebellum	SCAN
rs6545409	PSME4	cis	cerebellum	SCAN
rs6545409	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54701400-54709800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
3	chr2:54702200-54712200	Enhancers	Fetal Heart	heart
4	chr2:54702400-54712000	Enhancers	Colon Smooth Muscle	Colon
5	chr2:54703600-54710400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:54704400-54710400	Enhancers	Right Atrium	heart
7	chr2:54705000-54710400	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr2:54705200-54709800	Enhancers	Stomach Smooth Muscle	stomach
9	chr2:54705200-54710000	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:54705200-54712400	Enhancers	Brain Hippocampus Middle	brain
11	chr2:54705400-54710000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:54705600-54710000	Weak transcription	Small Intestine	intestine
13	chr2:54705800-54709800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:54706800-54711600	Enhancers	HSMMtube	muscle
15	chr2:54707000-54710400	Enhancers	Fetal Muscle Leg	muscle
16	chr2:54707200-54710600	Enhancers	Brain Angular Gyrus	brain
17	chr2:54707200-54711200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:54707200-54711400	Enhancers	Ovary	ovary
19	chr2:54707200-54712000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:54707200-54712200	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:54707200-54712400	Enhancers	Brain Substantia Nigra	brain
22	chr2:54707400-54709800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:54707400-54709800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:54707600-54709800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:54707600-54717600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:54707800-54709800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:54707800-54709800	Enhancers	NHDF-Ad	bronchial
28	chr2:54707800-54710200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:54707800-54712000	Enhancers	Psoas Muscle	Psoas
30	chr2:54707800-54720800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:54708000-54712400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:54708200-54710200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:54708200-54710400	Enhancers	Left Ventricle	heart
34	chr2:54708200-54711800	Weak transcription	Stomach Mucosa	stomach
35	chr2:54708400-54710400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:54708600-54709800	Weak transcription	Gastric	stomach
37	chr2:54708600-54710000	Weak transcription	Esophagus	oesophagus
38	chr2:54708600-54710000	Weak transcription	Pancreas	Pancrea
39	chr2:54708800-54710600	Enhancers	Fetal Stomach	stomach
40	chr2:54708800-54711000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:54708800-54712000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:54708800-54712000	Genic enhancers	Fetal Lung	lung
43	chr2:54709000-54709800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:54709000-54710000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:54709000-54710400	Enhancers	A549	lung
46	chr2:54709000-54711400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:54709000-54712200	Enhancers	Brain Anterior Caudate	brain
48	chr2:54709000-54712400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:54709200-54709800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:54709200-54710000	Enhancers	Aorta	Aorta

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