Variant report

Variant	rs1207866
Chromosome Location	chr7:78401341-78401342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1012955	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244070	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029495	1.00[ASN][1000 genomes]
rs10485911	1.00[CHD][hapmap]
rs10953690	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207863	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207864	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207865	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1207894	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211415	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211690	0.80[AMR][1000 genomes]
rs12705771	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496767	1.00[CHD][hapmap]
rs17151525	1.00[CHD][hapmap]
rs17151530	0.87[CEU][hapmap]
rs17450323	1.00[CHD][hapmap]
rs1989977	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989978	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246458	0.80[EUR][1000 genomes]
rs246463	0.87[CEU][hapmap]
rs246464	0.87[CEU][hapmap]
rs2525808	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]
rs2774059	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37847	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37848	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37850	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs37860	0.87[CEU][hapmap]
rs37862	0.87[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs37863	0.87[CEU][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs37865	0.87[CEU][hapmap]
rs37868	0.87[CEU][hapmap]
rs37871	0.87[CEU][hapmap]
rs37872	0.87[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs37873	0.87[CEU][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs37875	0.87[CEU][hapmap]
rs37877	0.87[CEU][hapmap]
rs37881	1.00[ASN][1000 genomes]
rs37884	0.87[CEU][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs37887	1.00[ASN][1000 genomes]
rs39731	0.87[CEU][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4730487	0.86[TSI][hapmap]
rs55917954	1.00[ASN][1000 genomes]
rs723294	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7780363	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886472	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886473	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886474	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970757	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[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	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	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
rs1207866	CACNA2D1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78400600-78403000	Weak transcription	Psoas Muscle	Psoas
2	chr7:78400800-78401400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:78400800-78401800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:78400800-78402000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:78400800-78402000	Enhancers	Brain Cingulate Gyrus	brain
6	chr7:78401000-78401600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:78401000-78401800	Enhancers	Brain Germinal Matrix	brain
8	chr7:78401000-78402000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr7:78401000-78402000	Enhancers	Brain Angular Gyrus	brain
10	chr7:78401000-78402600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr7:78401000-78402600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:78401000-78402600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr7:78401000-78402600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr7:78401000-78402600	Enhancers	Fetal Brain Male	brain
15	chr7:78401200-78401400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:78401200-78401600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:78401200-78401800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr7:78401200-78401800	Weak transcription	Brain Substantia Nigra	brain
19	chr7:78401200-78402600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:78401200-78402600	Weak transcription	Fetal Brain Female	brain

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