Variant report

Variant	rs10489407
Chromosome Location	chr1:186824113-186824114
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10732978	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737270	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752977	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752978	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752979	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798060	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798061	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911933	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10911934	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911937	0.90[JPT][hapmap]
rs2205897	0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4651330	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4651331	0.85[JPT][hapmap]
rs4651332	0.82[YRI][hapmap]
rs4651334	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425051	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425052	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425053	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669230	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682761	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685652	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687896	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6688584	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521601	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522183	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532616	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7541946	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489407	OCLM	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186800200-186827800	Weak transcription	NHEK	skin
2	chr1:186808600-186828200	Weak transcription	Pancreas	Pancrea
3	chr1:186808600-186830800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:186810400-186824800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:186815200-186844800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:186817600-186824600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:186817800-186839000	Weak transcription	Hela-S3	cervix
8	chr1:186818000-186831000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:186818000-186834600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:186818800-186828600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:186819000-186827800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:186819200-186824600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:186819200-186825400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:186819800-186824600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:186822800-186828200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:186823000-186828000	Weak transcription	Fetal Brain Male	brain
17	chr1:186823600-186824200	Enhancers	HUVEC	blood vessel
18	chr1:186823600-186824600	Weak transcription	Fetal Lung	lung
19	chr1:186823800-186825400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:186823800-186825800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:186823800-186826000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:186824000-186824200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:186824000-186824400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:186824000-186824600	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:186824000-186825400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:186824000-186826000	Weak transcription	A549	lung
27	chr1:186824000-186826200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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