Variant report

Variant	rs6769408
Chromosome Location	chr3:55895409-55895410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12633538	0.87[AMR][1000 genomes]
rs12636793	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1379710	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1458066	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056053	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17056061	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056065	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056081	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056090	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056093	0.81[ASN][1000 genomes]
rs17056098	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1902861	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35046325	0.88[AMR][1000 genomes]
rs55673265	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675302	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55682897	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55957219	1.00[ASN][1000 genomes]
rs55967115	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55971093	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56211981	0.84[AMR][1000 genomes]
rs57688760	1.00[ASN][1000 genomes]
rs58422259	1.00[ASN][1000 genomes]
rs59611401	1.00[ASN][1000 genomes]
rs62253660	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253661	0.87[AMR][1000 genomes]
rs62255821	1.00[ASN][1000 genomes]
rs62255831	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255832	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255835	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256771	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256772	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256773	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256774	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256778	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6445755	0.88[ASN][1000 genomes]
rs6763408	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766607	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790300	1.00[ASN][1000 genomes]
rs73073394	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs733509	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609626	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617166	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618265	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631779	1.00[ASN][1000 genomes]
rs7631846	1.00[ASN][1000 genomes]
rs7636943	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638901	1.00[ASN][1000 genomes]
rs7649504	0.80[EUR][1000 genomes]
rs897965	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9815155	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs993594	0.88[AMR][1000 genomes];0.83[EUR][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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv876815	chr3:55895409-55979964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55891800-55896400	Enhancers	Brain Germinal Matrix	brain
2	chr3:55892600-55896000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:55893000-55908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:55893400-55895800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:55893400-55896000	Weak transcription	Fetal Heart	heart
6	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:55894000-55901400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:55894200-55895800	Enhancers	Brain Substantia Nigra	brain
9	chr3:55894600-55901200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:55895000-55896400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:55895400-55896000	Weak transcription	Brain Cingulate Gyrus	brain

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