Variant report

Variant	rs7784056
Chromosome Location	chr7:78117387-78117388
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10156060	0.81[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs12670134	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]
rs1548868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978323	0.86[EUR][1000 genomes]
rs1990577	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2215935	0.80[AFR][1000 genomes]
rs2362611	0.87[EUR][1000 genomes]
rs3735442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996259	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs67578259	0.92[AFR][1000 genomes]
rs741254	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779312	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784896	0.80[LWK][hapmap]
rs7785241	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804932	0.90[YRI][hapmap]
rs7807727	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641412	0.84[LWK][hapmap]
rs975421	0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7784056	GTF2IRD1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78103000-78117600	Weak transcription	Fetal Brain Female	brain
2	chr7:78108800-78117400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:78108800-78118800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:78109000-78118200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:78109600-78117600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:78109600-78118600	Weak transcription	Fetal Heart	heart
7	chr7:78113600-78118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:78114800-78118400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:78114800-78127800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:78115000-78119000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:78115200-78118600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:78115400-78118600	Weak transcription	Fetal Brain Male	brain
13	chr7:78116200-78118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:78116400-78117400	Enhancers	HepG2	liver
15	chr7:78116600-78125600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:78116800-78117400	Active TSS	Brain Angular Gyrus	brain
17	chr7:78116800-78117600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:78116800-78118000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:78116800-78119600	Active TSS	Brain Anterior Caudate	brain
20	chr7:78116800-78119600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr7:78117000-78117400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr7:78117000-78118200	Enhancers	Brain Germinal Matrix	brain
23	chr7:78117000-78118200	Weak transcription	Ovary	ovary
24	chr7:78117000-78118600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:78117000-78118800	Weak transcription	Small Intestine	intestine
26	chr7:78117200-78117400	Active TSS	Brain Hippocampus Middle	brain

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