Variant report

Variant	rs12155286
Chromosome Location	chr7:78114661-78114662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10238963	0.83[GIH][hapmap]
rs10260232	0.85[MKK][hapmap]
rs10279188	0.80[CEU][hapmap]
rs10279625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10485896	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs11763781	0.80[CEU][hapmap]
rs11975402	0.80[CEU][hapmap]
rs12705478	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[AMR][1000 genomes]
rs12705481	0.80[CEU][hapmap];0.88[AMR][1000 genomes]
rs12705483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224634	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13237945	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs17435216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71573385	0.84[AMR][1000 genomes]
rs71573386	0.84[AMR][1000 genomes]
rs7807844	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	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
rs12155286	GTF2IRD1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78103000-78117600	Weak transcription	Fetal Brain Female	brain
2	chr7:78103800-78115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:78104400-78116800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:78106600-78117000	Weak transcription	Brain Germinal Matrix	brain
5	chr7:78108400-78116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:78108800-78117400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:78108800-78118800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:78109000-78118200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:78109600-78117600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:78109600-78118600	Weak transcription	Fetal Heart	heart
11	chr7:78113600-78118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:78113800-78114800	Enhancers	Brain Anterior Caudate	brain
13	chr7:78113800-78115800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:78114000-78114800	Enhancers	Brain Cingulate Gyrus	brain
15	chr7:78114400-78114800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:78114400-78116000	Weak transcription	Brain Substantia Nigra	brain
17	chr7:78114600-78116400	Weak transcription	Brain Hippocampus Middle	brain

Quick Search:

Input of quick search could be:

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

what's new

Quick links