Variant report

Variant	rs12782979
Chromosome Location	chr10:4387643-4387644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10508281	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10751967	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10795157	0.90[ASN][1000 genomes]
rs10795158	0.90[ASN][1000 genomes]
rs10904235	0.90[ASN][1000 genomes]
rs10904236	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10904237	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10904238	0.95[EUR][1000 genomes]
rs10904245	0.91[EUR][1000 genomes]
rs10904247	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs11252474	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252476	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11252477	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11252478	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11252482	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11252491	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11252496	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11252503	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs12217543	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12219673	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12569665	0.93[EUR][1000 genomes]
rs1571129	0.92[ASN][1000 genomes]
rs1926808	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1926809	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2025774	0.89[CEU][hapmap];0.89[CHB][hapmap];0.87[TSI][hapmap]
rs2025775	0.81[EUR][1000 genomes]
rs2182586	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4261192	0.89[ASN][1000 genomes]
rs4265499	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4272695	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4550130	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4564225	0.93[ASN][1000 genomes]
rs4881317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60075506	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61829444	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6601835	0.89[ASN][1000 genomes]
rs6601836	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601840	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7082820	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72766472	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7900466	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7902863	0.89[ASN][1000 genomes]
rs7919885	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs927897	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9633757	0.81[EUR][1000 genomes];0.97[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	nsv894786	chr10:4385379-4441989	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12782979	FAM115A	trans	brain	seeQTL
rs12782979	VPS13A	trans	brain	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4382400-4389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:4385200-4387800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:4385200-4388000	Enhancers	Fetal Lung	lung
4	chr10:4386000-4388000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:4386000-4388000	Enhancers	HMEC	breast
6	chr10:4386000-4388200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:4386000-4388400	Enhancers	Fetal Heart	heart
8	chr10:4386000-4388600	Enhancers	NHLF	lung
9	chr10:4386000-4388800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:4386000-4388800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:4386000-4388800	Enhancers	NHDF-Ad	bronchial
12	chr10:4386200-4387800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:4386200-4387800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr10:4386200-4388400	Enhancers	Fetal Stomach	stomach
15	chr10:4386200-4388600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:4386200-4388600	Enhancers	Rectal Smooth Muscle	rectum
17	chr10:4386200-4388800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:4386600-4388000	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr10:4386600-4394600	Weak transcription	Left Ventricle	heart
20	chr10:4386800-4387800	Enhancers	HSMM	muscle
21	chr10:4387000-4388600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr10:4387200-4388400	Enhancers	Brain Angular Gyrus	brain
23	chr10:4387200-4388400	Enhancers	Stomach Smooth Muscle	stomach
24	chr10:4387200-4388400	Enhancers	A549	lung
25	chr10:4387400-4387800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:4387400-4387800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr10:4387400-4388200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr10:4387400-4388600	Enhancers	Brain Anterior Caudate	brain
29	chr10:4387400-4388800	Enhancers	Colon Smooth Muscle	Colon
30	chr10:4387400-4394400	Weak transcription	Aorta	Aorta
31	chr10:4387600-4387800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr10:4387600-4388000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:4387600-4388000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr10:4387600-4388400	Weak transcription	Adipose Nuclei	Adipose
35	chr10:4387600-4388400	Enhancers	HSMMtube	muscle
36	chr10:4387600-4388400	Enhancers	NHEK	skin
37	chr10:4387600-4388600	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:4387600-4388600	Enhancers	Hela-S3	cervix
39	chr10:4387600-4388800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:4387600-4389800	Weak transcription	Psoas Muscle	Psoas
41	chr10:4387600-4394400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links