Variant report

Variant	rs7789655
Chromosome Location	chr7:86481013-86481014
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10270673	0.82[EUR][1000 genomes]
rs12704299	0.90[CEU][hapmap]
rs17126	0.90[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2282966	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6465088	0.90[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs67263053	0.82[ASN][1000 genomes]
rs6944519	0.84[EUR][1000 genomes]
rs6944719	0.82[EUR][1000 genomes]
rs6965383	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs6976877	1.00[CEU][hapmap]
rs7781178	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7781414	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs7788695	0.82[EUR][1000 genomes]
rs7807203	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7789655	SEMA3D	cis	cerebellum	SCAN
rs7789655	DMTF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86460800-86492800	Weak transcription	Brain Germinal Matrix	brain
2	chr7:86461000-86495400	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:86465600-86496800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:86466000-86486600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:86467000-86497400	Weak transcription	Fetal Brain Female	brain
6	chr7:86469200-86496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:86475800-86496600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:86479200-86488200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:86479600-86481600	Strong transcription	Brain Anterior Caudate	brain
10	chr7:86480600-86481400	Strong transcription	Brain Angular Gyrus	brain
11	chr7:86480600-86481400	Strong transcription	Brain Substantia Nigra	brain
12	chr7:86480600-86481600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr7:86480600-86481600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr7:86480800-86481200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr7:86480800-86481200	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr7:86480800-86481400	Strong transcription	Brain Cingulate Gyrus	brain
17	chr7:86481000-86481400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr7:86481000-86481400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:86481000-86481600	Enhancers	H1 Cell Line	embryonic stem cell

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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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