Variant report

Variant	rs1877027
Chromosome Location	chr2:63072430-63072431
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12612046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613453	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614162	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17347994	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17407696	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17432566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs17432580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17432615	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17432663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17473084	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17598689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17598881	0.95[ASN][1000 genomes]
rs17657533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17657580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1877027	PEX13	cis	cerebellum	SCAN
rs1877027	OTX1	cis	Whole Blood	GTEx
rs1877027	TMEM17	cis	cerebellum	SCAN
rs1877027	AFTPH	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
4	chr2:63040600-63082000	Weak transcription	Lung	lung
5	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
9	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:63055000-63082000	Weak transcription	Esophagus	oesophagus
12	chr2:63056400-63081800	Weak transcription	NHLF	lung
13	chr2:63060800-63081000	Weak transcription	Left Ventricle	heart
14	chr2:63060800-63081800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:63061000-63073000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:63061000-63073200	Weak transcription	NH-A	brain
17	chr2:63061000-63080400	Weak transcription	Aorta	Aorta
18	chr2:63061200-63080800	Weak transcription	Psoas Muscle	Psoas
19	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:63061400-63080400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:63061600-63072600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:63061600-63082000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:63061800-63073200	Weak transcription	Primary B cells from cord blood	blood
25	chr2:63061800-63080800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:63062000-63072600	Weak transcription	Adipose Nuclei	Adipose
27	chr2:63062000-63073000	Weak transcription	Fetal Kidney	kidney
28	chr2:63062000-63073000	Weak transcription	Fetal Lung	lung
29	chr2:63062000-63076400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:63062000-63080600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:63062000-63081200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:63062000-63082400	Weak transcription	HMEC	breast
33	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:63062200-63072800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:63062200-63073000	Weak transcription	Fetal Brain Female	brain
36	chr2:63062200-63073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:63062200-63076400	Weak transcription	Osteobl	bone
38	chr2:63062200-63080600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:63062400-63073200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:63063000-63081800	Weak transcription	Fetal Stomach	stomach
41	chr2:63063200-63075800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:63070800-63072600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:63070800-63073200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:63071200-63073400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:63071200-63073400	Strong transcription	Ovary	ovary
46	chr2:63071200-63074000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:63071200-63097200	Strong transcription	HepG2	liver
48	chr2:63071400-63072600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr2:63071400-63072800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:63071400-63073600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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