Variant report

Variant	rs7808864
Chromosome Location	chr7:83723347-83723348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10259508	0.82[EUR][1000 genomes]
rs10261415	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10263314	0.84[CEU][hapmap]
rs10808306	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12707619	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1468345	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1468346	0.81[EUR][1000 genomes]
rs2040872	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2067693	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2158566	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2189847	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2527037	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691698	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2691700	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3801655	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4141151	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs447	0.84[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs464	0.83[GIH][hapmap]
rs6467988	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6651129	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6964546	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6977099	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6978184	0.84[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap]
rs7781923	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7783472	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7785708	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7793598	0.83[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7808864	CACNA2D1	cis	parietal	SCAN
rs7808864	SEMA3D	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83715600-83730200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:83715600-83731400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:83718400-83735000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:83720800-83723400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:83721600-83735200	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:83721800-83723800	Weak transcription	Fetal Brain Male	brain
7	chr7:83721800-83726800	Enhancers	Primary T cells from cord blood	blood
8	chr7:83721800-83728600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:83722000-83724600	Weak transcription	Pancreas	Pancrea
10	chr7:83722000-83726400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:83722200-83723400	Enhancers	Dnd41	blood
12	chr7:83722200-83724800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:83722200-83724800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:83722200-83724800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:83722200-83734000	Weak transcription	Fetal Lung	lung
16	chr7:83722200-83734200	Weak transcription	NHDF-Ad	bronchial
17	chr7:83722200-83735800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:83722200-83737600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:83722200-83738400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:83722600-83723800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:83722800-83724800	Weak transcription	Fetal Heart	heart
22	chr7:83723000-83724200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:83723200-83723400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:83723200-83723400	Enhancers	HepG2	liver

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