Variant report

Variant	rs7782295
Chromosome Location	chr7:136969496-136969497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10268741	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11765480	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1367590	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1473355	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1835534	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1880790	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1882066	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs322256	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs322257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3959914	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3959915	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6943993	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6950835	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6972523	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9969157	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][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	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831149	chr7:136831665-137006468	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv889238	chr7:136915059-136989606	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv889239	chr7:136923730-136994013	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7782295	C7orf49	cis	parietal	SCAN
rs7782295	LRGUK	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136938200-136980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:136952200-136971000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:136961400-136973600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:136961400-136980600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:136965800-136969600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:136967600-136969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:136968000-136973600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:136968200-136970600	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:136968200-136971600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:136968200-136971600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:136968400-136971800	Weak transcription	Brain Angular Gyrus	brain
12	chr7:136968400-136971800	Weak transcription	Brain Substantia Nigra	brain
13	chr7:136968600-136971400	Weak transcription	Brain Anterior Caudate	brain
14	chr7:136968600-136989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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