Variant report

Variant	rs5003961
Chromosome Location	chr7:78072444-78072445
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1017149	1.00[CEU][hapmap]
rs10228924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10241911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10259327	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]
rs11974883	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]
rs12670815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];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]
rs2362598	0.83[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2885552	1.00[ASW][hapmap];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4501511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515471	1.00[ASW][hapmap];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]
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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs5003961	PRR18	trans	brain	seeQTL
rs5003961	GLDN	trans	brain	seeQTL
rs5003961	SIRT2	trans	brain	seeQTL
rs5003961	CDC20	trans	brain	seeQTL
rs5003961	CD97	trans	brain	seeQTL
rs5003961	NINJ2	trans	brain	seeQTL
rs5003961	TIMP2	trans	brain	seeQTL
rs5003961	VWA1	trans	brain	seeQTL
rs5003961	TYMS	trans	brain	seeQTL
rs5003961	FOLH1B	trans	brain	seeQTL
rs5003961	BTBD16	trans	brain	seeQTL
rs5003961	GAL3ST1	trans	brain	seeQTL
rs5003961	COL9A2	trans	brain	seeQTL
rs5003961	ATP10B	trans	brain	seeQTL
rs5003961	MAG	trans	brain	seeQTL
rs5003961	PPAP2C	trans	brain	seeQTL
rs5003961	KCNH8	trans	brain	seeQTL
rs5003961	RBP7	trans	brain	seeQTL
rs5003961	PDE6B	trans	brain	seeQTL
rs5003961	CNTNAP4	trans	brain	seeQTL
rs5003961	ELOVL1	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78067000-78079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:78071000-78073600	Enhancers	Brain Anterior Caudate	brain
3	chr7:78071200-78072800	Enhancers	Brain Angular Gyrus	brain
4	chr7:78071200-78072800	Enhancers	Brain Hippocampus Middle	brain
5	chr7:78071400-78073000	Enhancers	Brain Substantia Nigra	brain
6	chr7:78071400-78073600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr7:78071600-78072800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:78071600-78073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:78072000-78072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:78072200-78073200	Enhancers	Fetal Heart	heart
11	chr7:78072400-78073200	Enhancers	Brain Cingulate Gyrus	brain

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