Variant report

Variant	rs1883610
Chromosome Location	chr6:38340099-38340100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12191714	0.86[JPT][hapmap]
rs12206324	0.86[JPT][hapmap]
rs12206905	0.86[JPT][hapmap]
rs12212983	1.00[JPT][hapmap]
rs12215850	0.86[JPT][hapmap]
rs1983605	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs28445226	0.86[JPT][hapmap]
rs4236058	0.86[JPT][hapmap]
rs4711542	0.86[JPT][hapmap]
rs4711546	0.86[JPT][hapmap]
rs4714152	0.86[JPT][hapmap]
rs4714157	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs6899746	0.86[JPT][hapmap]
rs6901086	0.86[JPT][hapmap]
rs6904723	0.86[JPT][hapmap]
rs6933268	0.86[JPT][hapmap]
rs6933758	0.86[JPT][hapmap]
rs6940319	0.86[JPT][hapmap]
rs742515	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs7748599	0.86[JPT][hapmap]
rs7749685	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs7759629	0.86[JPT][hapmap]
rs7766214	0.86[JPT][hapmap]
rs7770868	0.86[JPT][hapmap]
rs871183	0.86[JPT][hapmap]
rs9349073	0.86[JPT][hapmap]
rs9357272	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9380739	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9380743	0.86[JPT][hapmap]
rs9394492	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9394495	0.86[JPT][hapmap]
rs9470885	0.86[JPT][hapmap]
rs9470888	0.86[JPT][hapmap]
rs9470891	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1883610	GLO1	cis	cerebellum	SCAN
rs1883610	NFYA	cis	parietal	SCAN
rs1883610	PDE1B	trans	brain	seeQTL
rs1883610	CPNE5	cis	parietal	SCAN
rs1883610	GLO1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38333600-38342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:38338200-38341400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:38338600-38340800	Enhancers	Ovary	ovary
4	chr6:38338800-38341400	Enhancers	NHDF-Ad	bronchial
5	chr6:38339200-38340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:38339400-38340400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:38339400-38340600	Weak transcription	Fetal Kidney	kidney
8	chr6:38339400-38340800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:38339400-38342200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:38339400-38342400	Weak transcription	Brain Substantia Nigra	brain
11	chr6:38339400-38342400	Weak transcription	Psoas Muscle	Psoas
12	chr6:38339400-38342400	Weak transcription	Right Atrium	heart
13	chr6:38339400-38342400	Weak transcription	Right Ventricle	heart
14	chr6:38339400-38348200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:38339600-38340800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:38339600-38342400	Weak transcription	Adipose Nuclei	Adipose
17	chr6:38340000-38342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:38340000-38342600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:38340000-38342600	Weak transcription	HSMMtube	muscle
20	chr6:38340000-38344000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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