Variant report

Variant	rs17598881
Chromosome Location	chr2:63263931-63263932
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63263150..63266511-chr2:63267501..63271006,3	K562	blood:
2	chr2:63263370..63266087-chr2:63278699..63280951,3	K562	blood:
3	chr2:63262217..63266087-chr2:63277395..63281229,4	K562	blood:
4	chr2:63252312..63254872-chr2:63263064..63265744,2	K562	blood:

Variant related genes	Relation type
ENSG00000115507	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12612046	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614162	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	0.95[ASN][1000 genomes]
rs17432559	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432580	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432615	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	1.00[AFR][1000 genomes]
rs17598689	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657533	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17598881	OTX1	cis	Whole Blood	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63219200-63269800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus
4	chr2:63224600-63272000	Weak transcription	NHLF	lung
5	chr2:63228000-63267600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:63238400-63267600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:63240800-63271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:63240800-63272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:63244000-63274400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:63244200-63274600	Weak transcription	Pancreas	Pancrea
11	chr2:63248800-63269400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:63248800-63271600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:63252600-63271600	Weak transcription	Fetal Stomach	stomach
14	chr2:63255000-63271800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:63255400-63272600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:63255600-63272000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:63255800-63265400	Weak transcription	Left Ventricle	heart
18	chr2:63255800-63265600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:63256000-63270400	Weak transcription	Primary B cells from cord blood	blood
20	chr2:63256800-63264600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:63256800-63265800	Weak transcription	HSMM	muscle
22	chr2:63256800-63265800	Weak transcription	NHDF-Ad	bronchial
23	chr2:63256800-63271800	Weak transcription	Ovary	ovary
24	chr2:63256800-63272200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:63256800-63272400	Weak transcription	Osteobl	bone
26	chr2:63256800-63275600	Weak transcription	HMEC	breast
27	chr2:63257000-63267600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:63257400-63264600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:63257600-63264800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:63259000-63264600	Weak transcription	Liver	Liver
31	chr2:63259000-63265800	Weak transcription	HepG2	liver
32	chr2:63259400-63265600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:63260800-63265600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:63262200-63270800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:63262200-63271800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:63262400-63275600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:63262600-63273600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:63263000-63267600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:63263000-63267600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:63263000-63270600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:63263000-63273200	Weak transcription	NH-A	brain
42	chr2:63263000-63276400	Weak transcription	A549	lung
43	chr2:63263200-63267600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:63263200-63267800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:63263200-63268800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:63263200-63270200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:63263600-63267800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:63263600-63273800	Weak transcription	HUVEC	blood vessel

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