Variant report

Variant	rs12046746
Chromosome Location	chr1:221635207-221635208
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1031674	0.90[ASN][1000 genomes]
rs11118738	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11118740	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12029151	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030169	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12032381	0.95[ASN][1000 genomes]
rs12038764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12041783	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12757436	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17010060	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010123	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1903138	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1903139	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34525999	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35616756	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35826842	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59313526	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6655923	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6657854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674252	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688377	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688476	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72629676	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544629	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12046746	C1orf115	cis	lymphoblastoid	seeQTL
rs12046746	MOSC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221632000-221635600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:221632200-221635600	Weak transcription	Osteobl	bone
3	chr1:221632200-221636200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr1:221632600-221635400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:221632600-221635400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:221632600-221635600	Weak transcription	HSMM	muscle
7	chr1:221633200-221636200	Weak transcription	Fetal Lung	lung
8	chr1:221634800-221635800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:221634800-221635800	Weak transcription	Psoas Muscle	Psoas
10	chr1:221635000-221636200	Enhancers	NHEK	skin
11	chr1:221635000-221636400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:221635200-221636200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:221635200-221636200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:221635200-221636200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:221635200-221636400	Enhancers	HMEC	breast

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