Variant report

Variant	rs759334
Chromosome Location	chr7:78118506-78118507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10271232	0.81[AFR][1000 genomes]
rs4996260	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs759333	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs759335	0.80[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs7779732	0.80[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs759334	GTF2IRD1	cis	parietal	SCAN
rs759334	LOC100133091	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78108800-78118800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:78109600-78118600	Weak transcription	Fetal Heart	heart
3	chr7:78113600-78118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:78114800-78127800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:78115000-78119000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:78115200-78118600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:78115400-78118600	Weak transcription	Fetal Brain Male	brain
8	chr7:78116200-78118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:78116600-78125600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:78116800-78119600	Active TSS	Brain Anterior Caudate	brain
11	chr7:78116800-78119600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr7:78117000-78118600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:78117000-78118800	Weak transcription	Small Intestine	intestine
14	chr7:78117400-78119400	Active TSS	Brain Substantia Nigra	brain
15	chr7:78117600-78119200	Active TSS	Brain Hippocampus Middle	brain
16	chr7:78117600-78119400	Active TSS	Fetal Brain Female	brain
17	chr7:78118200-78118600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr7:78118200-78118600	Enhancers	NH-A	brain
19	chr7:78118200-78118800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:78118200-78119200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:78118200-78119400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:78118200-78119600	Active TSS	Brain Angular Gyrus	brain
23	chr7:78118200-78119600	Active TSS	Ovary	ovary
24	chr7:78118400-78118600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:78118400-78118800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:78118400-78118800	Active TSS	Brain Germinal Matrix	brain
27	chr7:78118400-78119400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:78118400-78119400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:78118400-78119400	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr7:78118400-78119600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr7:78118400-78119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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