Variant report

Variant	rs3799000
Chromosome Location	chr6:69715114-69715115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12194774	0.83[CEU][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes]
rs12194946	0.83[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes]
rs12213405	0.82[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs13192798	0.93[AFR][1000 genomes]
rs1336635	0.93[AFR][1000 genomes]
rs1336636	0.93[AFR][1000 genomes]
rs1336654	0.83[JPT][hapmap]
rs1415029	0.82[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs1556756	0.93[AFR][1000 genomes]
rs3757049	0.91[JPT][hapmap]
rs3798999	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799002	0.83[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs3799019	0.82[JPT][hapmap]
rs7756040	0.81[CEU][hapmap]
rs7760307	0.81[CEU][hapmap]
rs9360369	0.83[JPT][hapmap]
rs9454670	0.81[AFR][1000 genomes]
rs9454674	0.82[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]

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:18 , 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

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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