Variant report

Variant	rs12520102
Chromosome Location	chr5:54035929-54035930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53812457..53815422-chr5:54035928..54038801,2	MCF-7	breast:
2	chr5:54014127..54018411-chr5:54034085..54037239,3	K562	blood:
3	chr5:54014127..54017064-chr5:54035440..54037239,2	K562	blood:

Variant related genes	Relation type
ENSG00000178996	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10077227	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10077228	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10940421	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741898	0.91[ASN][1000 genomes]
rs13180905	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1445837	0.91[ASN][1000 genomes]
rs1445838	0.91[ASN][1000 genomes]
rs1445839	0.91[ASN][1000 genomes]
rs1867687	0.91[ASN][1000 genomes]
rs35207106	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4242043	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4367251	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4367252	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4367253	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410612	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4419552	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4487449	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4541609	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4596333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4639171	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4639172	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6872707	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6881842	0.92[ASN][1000 genomes]
rs6899028	0.90[ASN][1000 genomes]
rs7701622	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7710924	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7735360	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735378	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7736184	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs895329	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9292068	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880717	chr5:54025701-54106378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12520102	MOCS2	cis	cerebellum	SCAN
rs12520102	PELO	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54017000-54038000	Weak transcription	Aorta	Aorta
2	chr5:54032600-54037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:54032600-54038200	Weak transcription	Fetal Heart	heart
4	chr5:54032600-54038800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:54033800-54037200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:54034200-54037800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:54034200-54038200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:54034200-54038200	Weak transcription	HSMM	muscle
9	chr5:54034200-54038400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:54034200-54038400	Weak transcription	Fetal Lung	lung
11	chr5:54034200-54039000	Enhancers	NHDF-Ad	bronchial
12	chr5:54034200-54039600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:54034200-54040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:54034400-54036000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:54034400-54036000	Weak transcription	Spleen	Spleen
16	chr5:54034400-54036800	Weak transcription	Gastric	stomach
17	chr5:54034400-54037600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:54034400-54037600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:54034400-54037600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:54034400-54037600	Weak transcription	Osteobl	bone
21	chr5:54034400-54038200	Weak transcription	Adipose Nuclei	Adipose
22	chr5:54034400-54038200	Weak transcription	Left Ventricle	heart
23	chr5:54034400-54038200	Weak transcription	Small Intestine	intestine
24	chr5:54034400-54038200	Weak transcription	Stomach Mucosa	stomach
25	chr5:54034400-54039400	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:54034400-54039800	Weak transcription	Esophagus	oesophagus
27	chr5:54034400-54039800	Weak transcription	Fetal Stomach	stomach
28	chr5:54034400-54039800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:54034600-54036800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:54034600-54037400	Weak transcription	Hela-S3	cervix
31	chr5:54034600-54037600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:54034600-54037800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:54034600-54038000	Weak transcription	Placenta	Placenta
34	chr5:54034600-54038200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:54034600-54038200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:54034600-54038200	Weak transcription	Right Atrium	heart
37	chr5:54034600-54038200	Weak transcription	Right Ventricle	heart
38	chr5:54034600-54038200	Weak transcription	HUVEC	blood vessel
39	chr5:54034600-54039200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:54034600-54039600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:54034600-54039800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:54034600-54041400	Weak transcription	Lung	lung
43	chr5:54034800-54037600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr5:54034800-54037600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:54034800-54037600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr5:54034800-54037800	Enhancers	K562	blood
47	chr5:54034800-54038200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:54034800-54038200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:54034800-54039400	Weak transcription	Primary T cells from cord blood	blood
50	chr5:54035200-54038000	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links