Variant report

Variant	rs11974883
Chromosome Location	chr7:78068524-78068525
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1017149	1.00[CEU][hapmap]
rs10228924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10241911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10259327	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10259937	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10266615	1.00[CEU][hapmap]
rs12670815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080374	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2362596	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2885552	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4498477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4501511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5003961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759424	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7783735	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7788276	1.00[EUR][1000 genomes]
rs7796439	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7802125	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7802920	1.00[EUR][1000 genomes]
rs7806209	0.84[AMR][1000 genomes];1.00[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11974883	ISG20	trans	brain	seeQTL
rs11974883	OAS3	trans	brain	seeQTL
rs11974883	IFI44	trans	brain	seeQTL
rs11974883	STAT1	trans	brain	seeQTL
rs11974883	IFI44L	trans	brain	seeQTL
rs11974883	MX1	trans	brain	seeQTL
rs11974883	IFIT3	trans	brain	seeQTL
rs11974883	GBP5	trans	brain	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78067000-78072400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:78067000-78079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:78067600-78068800	Enhancers	Brain Hippocampus Middle	brain
4	chr7:78067600-78071600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:78067800-78068600	Enhancers	Brain Angular Gyrus	brain
6	chr7:78068000-78068600	Enhancers	Brain Substantia Nigra	brain
7	chr7:78068000-78069200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:78068000-78071000	Weak transcription	Brain Anterior Caudate	brain
9	chr7:78068400-78068800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:78068400-78069200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr7:78068400-78069800	Weak transcription	Fetal Brain Female	brain
12	chr7:78068400-78071000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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