Variant report

Variant	rs17045941
Chromosome Location	chr2:54738392-54738393
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12477376	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12622708	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4519565	0.81[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4671223	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671224	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs4671952	0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6545428	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6717713	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717816	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68134840	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9309255	0.95[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17045941	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs17045941	VRK2	cis	cerebellum	SCAN
rs17045941	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
4	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
5	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
8	chr2:54730600-54739400	Weak transcription	HepG2	liver
9	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
11	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
13	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
14	chr2:54733600-54747000	Weak transcription	Gastric	stomach
15	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:54734600-54738400	Enhancers	Fetal Heart	heart
17	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:54735200-54740400	Enhancers	Left Ventricle	heart
19	chr2:54735600-54738400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:54735600-54738400	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:54735600-54738400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:54735600-54738600	Enhancers	Adipose Nuclei	Adipose
23	chr2:54735600-54738600	Enhancers	Brain Anterior Caudate	brain
24	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
25	chr2:54735800-54740600	Enhancers	Brain Hippocampus Middle	brain
26	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
27	chr2:54736600-54738400	Enhancers	HSMMtube	muscle
28	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:54736800-54738400	Enhancers	Ovary	ovary
30	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
31	chr2:54737200-54738400	Enhancers	Primary hematopoietic stem cells	blood
32	chr2:54737400-54738400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:54737400-54738400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr2:54737400-54738400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:54737400-54738400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:54737400-54738400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:54737400-54738400	Genic enhancers	NHDF-Ad	bronchial
38	chr2:54737400-54738600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:54737400-54738600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:54737400-54739200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
43	chr2:54737800-54738400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:54737800-54738400	Enhancers	A549	lung
45	chr2:54737800-54739000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:54737800-54739200	Weak transcription	Fetal Thymus	thymus
47	chr2:54737800-54739800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:54738000-54738400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:54738200-54738400	Enhancers	Placenta	Placenta
50	chr2:54738200-54738400	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links