Variant report

Variant	rs4129261
Chromosome Location	chr2:54706092-54706093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169422	0.93[EUR][1000 genomes]
rs10496032	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713258	0.92[EUR][1000 genomes]
rs12713259	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12990140	0.90[EUR][1000 genomes]
rs13034739	0.87[CEU][hapmap]
rs13387187	0.92[EUR][1000 genomes]
rs13390258	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13412585	0.92[EUR][1000 genomes]
rs35028480	0.80[EUR][1000 genomes]
rs6545408	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6710809	0.87[CEU][hapmap]
rs6740698	0.93[EUR][1000 genomes]
rs7566833	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7573223	0.91[EUR][1000 genomes]
rs7573805	0.92[EUR][1000 genomes]
rs7593062	0.87[CEU][hapmap]
rs7600596	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4129261	VRK2	cis	cerebellum	SCAN

Chromatin state (count:66 , 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	chr2:54698800-54707200	Weak transcription	Pancreas	Pancrea
4	chr2:54699200-54706200	Weak transcription	HUVEC	blood vessel
5	chr2:54699600-54706600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:54699600-54709200	Weak transcription	Aorta	Aorta
7	chr2:54699800-54707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:54699800-54709600	Weak transcription	Osteobl	bone
9	chr2:54701200-54707200	Weak transcription	Fetal Brain Male	brain
10	chr2:54701400-54709800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
12	chr2:54702200-54712200	Enhancers	Fetal Heart	heart
13	chr2:54702400-54708200	Enhancers	Adipose Nuclei	Adipose
14	chr2:54702400-54712000	Enhancers	Colon Smooth Muscle	Colon
15	chr2:54702800-54706400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54702800-54707800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54702800-54708400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:54702800-54709000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:54703200-54708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:54703600-54710400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:54703800-54709000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54703800-54709000	Weak transcription	Fetal Brain Female	brain
23	chr2:54703800-54709200	Weak transcription	Right Ventricle	heart
24	chr2:54704400-54706400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:54704400-54707600	Enhancers	Brain Anterior Caudate	brain
26	chr2:54704400-54709000	Weak transcription	A549	lung
27	chr2:54704400-54710400	Enhancers	Right Atrium	heart
28	chr2:54704600-54706400	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:54704800-54706400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:54704800-54706400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr2:54705000-54709200	Enhancers	Liver	Liver
32	chr2:54705000-54710400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr2:54705200-54706400	Enhancers	Brain Angular Gyrus	brain
34	chr2:54705200-54706400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:54705200-54707400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54705200-54709600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:54705200-54709600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:54705200-54709800	Enhancers	Stomach Smooth Muscle	stomach
39	chr2:54705200-54710000	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:54705200-54712400	Enhancers	Brain Hippocampus Middle	brain
41	chr2:54705400-54707200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:54705400-54708000	Enhancers	NHLF	lung
43	chr2:54705400-54709600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:54705400-54710000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:54705600-54706400	Weak transcription	Lung	lung
46	chr2:54705600-54707200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:54705600-54708000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:54705600-54708600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:54705600-54708800	Weak transcription	Fetal Stomach	stomach
50	chr2:54705600-54709000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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