Variant report

Variant	rs2525808
Chromosome Location	chr7:78395320-78395321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10244070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10485911	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10953690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1207863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1207864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1207865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1207866	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1207867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1207894	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1211415	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12705771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1496767	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17151525	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17151530	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs17385455	1.00[CHB][hapmap]
rs17450323	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1989977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1989978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs246458	0.81[AMR][1000 genomes]
rs246463	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs246464	0.87[CEU][hapmap]
rs2774059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs37847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs37848	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs37850	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs37860	0.87[CEU][hapmap]
rs37862	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs37863	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs37865	0.87[CEU][hapmap]
rs37868	0.87[CEU][hapmap]
rs37871	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs37872	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs37873	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs37875	0.87[CEU][hapmap]
rs37877	0.87[CEU][hapmap]
rs37884	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap]
rs39731	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4730487	0.86[TSI][hapmap]
rs723294	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7780363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs886472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs886473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs886474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs970757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][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	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
2	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
3	nsv1019355	chr7:78319575-78399845	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv607657	chr7:78329795-78483211	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2525808	CACNA2D1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78386200-78397600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:78391000-78395400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:78391800-78398800	Weak transcription	Pancreas	Pancrea
4	chr7:78393600-78396200	Enhancers	Brain Hippocampus Middle	brain
5	chr7:78394000-78395800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr7:78394000-78396000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr7:78394000-78396600	Enhancers	Psoas Muscle	Psoas
8	chr7:78394000-78397000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:78394200-78395600	Enhancers	Brain Substantia Nigra	brain
10	chr7:78394400-78395400	Weak transcription	Fetal Brain Male	brain
11	chr7:78394400-78397400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:78394400-78397600	Weak transcription	Brain Angular Gyrus	brain
13	chr7:78394400-78397600	Weak transcription	Fetal Heart	heart
14	chr7:78394600-78396600	Weak transcription	Fetal Brain Female	brain
15	chr7:78395000-78395600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:78395000-78396200	Enhancers	Brain Anterior Caudate	brain
17	chr7:78395200-78395400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:78395200-78395600	Enhancers	Aorta	Aorta
19	chr7:78395200-78395800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr7:78395200-78395800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:78395200-78396200	Enhancers	Brain Cingulate Gyrus	brain
22	chr7:78395200-78396200	Enhancers	Colon Smooth Muscle	Colon

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