Variant report

Variant	rs6718276
Chromosome Location	chr2:54703979-54703980
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	chr2:54699717..54702089-chr2:54703143..54705442,2	K562	blood:

Extended variants
information (count: 31 )
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];0.96[ASN][1000 genomes]
rs10205013	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12477221	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17039554	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045917	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3087854	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35001659	0.88[EUR][1000 genomes]
rs4233950	0.83[EUR][1000 genomes]
rs4561702	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4635562	0.81[EUR][1000 genomes]
rs4671218	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671933	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671935	0.85[EUR][1000 genomes]
rs4671940	0.98[ASN][1000 genomes]
rs4671943	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58779052	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545409	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];0.90[ASN][1000 genomes]
rs72618659	0.90[EUR][1000 genomes]
rs72618660	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72618661	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618662	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7599380	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv3693290	chr2:54693204-54707562	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	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
rs6718276	PSME4	cis	cerebellum	SCAN
rs6718276	C2orf63	cis	cerebellum	SCAN
rs6718276	VRK2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54697200-54707200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54697200-54709600	Weak transcription	Placenta	Placenta
3	chr2:54698800-54705200	Weak transcription	Lung	lung
4	chr2:54698800-54707200	Weak transcription	Pancreas	Pancrea
5	chr2:54699000-54706000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54699200-54706200	Weak transcription	HUVEC	blood vessel
7	chr2:54699600-54706600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54699600-54709200	Weak transcription	Aorta	Aorta
9	chr2:54699800-54707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:54699800-54709600	Weak transcription	Osteobl	bone
11	chr2:54700600-54705600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:54700600-54705600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:54701200-54705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54701200-54707200	Weak transcription	Fetal Brain Male	brain
15	chr2:54701400-54704800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54701400-54705000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:54701400-54709800	Weak transcription	Brain Germinal Matrix	brain
18	chr2:54701600-54704800	Weak transcription	Fetal Stomach	stomach
19	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
20	chr2:54702200-54704000	Enhancers	Brain Anterior Caudate	brain
21	chr2:54702200-54712200	Enhancers	Fetal Heart	heart
22	chr2:54702400-54704600	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:54702400-54704800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:54702400-54705600	Enhancers	Brain Substantia Nigra	brain
25	chr2:54702400-54708200	Enhancers	Adipose Nuclei	Adipose
26	chr2:54702400-54712000	Enhancers	Colon Smooth Muscle	Colon
27	chr2:54702600-54704000	Enhancers	Gastric	stomach
28	chr2:54702600-54704000	Enhancers	Right Atrium	heart
29	chr2:54702600-54704200	Enhancers	Rectal Smooth Muscle	rectum
30	chr2:54702600-54705200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:54702600-54705200	Enhancers	HepG2	liver
32	chr2:54702800-54704400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:54702800-54705000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:54702800-54705200	Weak transcription	NHDF-Ad	bronchial
35	chr2:54702800-54706400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:54702800-54707800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:54702800-54708400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:54702800-54709000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:54703200-54708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:54703400-54704600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:54703400-54704600	Weak transcription	Psoas Muscle	Psoas
42	chr2:54703400-54705200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:54703400-54705200	Weak transcription	Spleen	Spleen
44	chr2:54703600-54704400	Enhancers	A549	lung
45	chr2:54703600-54704800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54703600-54705200	Weak transcription	Brain Angular Gyrus	brain
47	chr2:54703600-54705200	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:54703600-54705200	Enhancers	Fetal Intestine Large	intestine
49	chr2:54703600-54705200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:54703600-54710400	Weak transcription	H9 Cell Line	embryonic stem cell

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