Variant report

Variant	rs1324965
Chromosome Location	chr6:163429010-163429011
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10945871	0.93[EUR][1000 genomes]
rs1408706	0.86[ASN][1000 genomes]
rs1536034	0.86[ASN][1000 genomes]
rs2025547	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147654	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182052	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235943	0.92[EUR][1000 genomes]
rs4235944	0.93[EUR][1000 genomes]
rs4559072	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4709669	0.93[EUR][1000 genomes]
rs4709670	0.94[EUR][1000 genomes]
rs4709673	0.98[ASN][1000 genomes]
rs485964	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs501276	0.92[ASN][1000 genomes]
rs502478	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs503173	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs526117	0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs529106	0.91[ASN][1000 genomes]
rs532302	0.81[ASN][1000 genomes]
rs542381	0.83[ASN][1000 genomes]
rs545584	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs545846	0.81[ASN][1000 genomes]
rs546769	0.81[ASN][1000 genomes]
rs577874	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6909464	0.96[EUR][1000 genomes]
rs6941873	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7743777	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7746358	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7747404	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7751960	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7761803	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768238	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9346946	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9347714	0.85[EUR][1000 genomes]
rs9355420	0.92[ASN][1000 genomes]
rs9356092	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9364683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365528	0.94[EUR][1000 genomes]
rs942634	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917926	chr6:162646457-163609259	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1030546	chr6:162748287-163475085	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv538518	chr6:162748287-163475085	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv605159	chr6:162800156-163479507	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv529089	chr6:163129464-163516451	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030116	chr6:163273707-163525678	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1020900	chr6:163302262-163517812	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv916587	chr6:163337791-163606120	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv464126	chr6:163361196-163432364	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv605186	chr6:163361196-163432364	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1021433	chr6:163375760-163509866	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1324965	IGF2R	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163421400-163429600	Weak transcription	Pancreas	Pancrea
2	chr6:163428400-163429200	Enhancers	Brain Hippocampus Middle	brain
3	chr6:163428400-163429800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:163428600-163430000	Enhancers	Fetal Lung	lung
5	chr6:163428800-163430000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:163429000-163429200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:163429000-163429200	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:163429000-163429400	Weak transcription	Brain Anterior Caudate	brain

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