Variant report

Variant	rs12670134
Chromosome Location	chr7:78112998-78112999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1548868	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978323	0.86[EUR][1000 genomes]
rs1990577	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2362611	0.87[EUR][1000 genomes]
rs3735442	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4996259	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs741254	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741255	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779312	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7784056	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785241	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807727	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

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
rs12670134	GTF2IRD1	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr7:78105600-78113800	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:78106200-78113200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:78106400-78113600	Weak transcription	Brain Substantia Nigra	brain
7	chr7:78106600-78114000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:78106600-78117000	Weak transcription	Brain Germinal Matrix	brain
9	chr7:78108400-78116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:78108800-78117400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:78108800-78118800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:78109000-78118200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:78109200-78114400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:78109600-78117600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:78109600-78118600	Weak transcription	Fetal Heart	heart

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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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