Variant report

Variant	rs10947742
Chromosome Location	chr6:38478945-38478946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10947741	0.85[ASN][1000 genomes]
rs10947743	0.95[ASN][1000 genomes]
rs2748153	1.00[CEU][hapmap]
rs2748155	1.00[CEU][hapmap]
rs2748156	0.90[JPT][hapmap]
rs2748158	1.00[CEU][hapmap]
rs2814886	1.00[CEU][hapmap]
rs4141854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4631264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6900106	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910904	0.85[CHB][hapmap]
rs6924443	0.90[JPT][hapmap]
rs6938737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724242	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7752972	0.91[ASN][1000 genomes]
rs7753374	0.91[ASN][1000 genomes]
rs7761154	0.89[JPT][hapmap]
rs9296252	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9357277	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9366965	0.91[ASN][1000 genomes]
rs9369065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9394513	0.90[ASN][1000 genomes]
rs9394514	0.88[ASN][1000 genomes]
rs9394515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9462439	0.91[ASN][1000 genomes]
rs9462441	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9462442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9470889	1.00[CEU][hapmap]
rs9470902	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38468600-38486400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:38471600-38484200	Weak transcription	Right Atrium	heart
6	chr6:38471600-38493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:38472000-38482400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:38472000-38493800	Weak transcription	Lung	lung
9	chr6:38472400-38481800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:38476600-38499800	Weak transcription	Pancreas	Pancrea
11	chr6:38476800-38481400	Weak transcription	Fetal Brain Male	brain
12	chr6:38476800-38481800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:38476800-38498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:38477000-38481600	Weak transcription	Brain Anterior Caudate	brain
15	chr6:38477400-38482400	Weak transcription	Fetal Stomach	stomach
16	chr6:38477800-38498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:38478000-38480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:38478000-38481200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:38478000-38482200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:38478000-38484800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:38478000-38484800	Weak transcription	Fetal Lung	lung
22	chr6:38478000-38485000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:38478000-38485000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:38478000-38485200	Weak transcription	Gastric	stomach
25	chr6:38478000-38494800	Weak transcription	Fetal Kidney	kidney
26	chr6:38478200-38480200	Weak transcription	NHLF	lung
27	chr6:38478200-38481800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:38478200-38482200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:38478200-38484200	Weak transcription	Ovary	ovary
30	chr6:38478200-38484800	Weak transcription	NHDF-Ad	bronchial
31	chr6:38478400-38486200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:38478800-38479000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:38478800-38480000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:38478800-38480000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links