Variant report

Variant	rs3799001
Chromosome Location	chr6:69715266-69715267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10485429	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10485430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10945150	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11751150	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11754397	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11962923	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12529202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12529244	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs17401221	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2785571	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2793457	0.94[CEU][hapmap]
rs3757048	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799009	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55924387	0.84[AMR][1000 genomes]
rs60671712	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62416762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62416764	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62416780	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62416804	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62416805	0.81[AMR][1000 genomes]
rs62416808	0.84[AMR][1000 genomes]
rs62418324	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9446083	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69685800-69758800	Weak transcription	Fetal Brain Male	brain
2	chr6:69688200-69721200	Weak transcription	Left Ventricle	heart
3	chr6:69692000-69716600	Weak transcription	Fetal Stomach	stomach
4	chr6:69696400-69715400	Weak transcription	Aorta	Aorta
5	chr6:69701000-69723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:69701000-69737600	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:69701200-69721200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:69701200-69724400	Weak transcription	Brain Germinal Matrix	brain
9	chr6:69702400-69728600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:69702400-69737600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:69702600-69723800	Weak transcription	Brain Substantia Nigra	brain
12	chr6:69703800-69719400	Weak transcription	Fetal Brain Female	brain
13	chr6:69704800-69721600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:69706400-69720800	Weak transcription	Fetal Lung	lung
15	chr6:69706600-69721600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:69711600-69717600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:69713000-69721400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:69714600-69715600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:69715200-69715600	Enhancers	NH-A	brain

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