Variant report

Variant	rs464
Chromosome Location	chr7:83786460-83786461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10261415	0.90[CHB][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs10263314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10808306	0.90[CHB][hapmap]
rs2067693	0.90[CHB][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2158566	0.89[CHB][hapmap]
rs3801655	0.90[CHB][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs447	0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap]
rs6467988	0.90[CHB][hapmap]
rs6964546	0.90[CHB][hapmap]
rs6977516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978184	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs7781923	0.90[CHB][hapmap]
rs7783472	0.90[CHB][hapmap]
rs7785708	0.90[CHB][hapmap]
rs7793598	0.90[CHB][hapmap];0.83[GIH][hapmap]
rs7804563	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7808864	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3692934	chr7:83778360-83786460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv442055	chr7:83782433-83786688	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv519788	chr7:83782435-83786460	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv517852	chr7:83782435-83794756	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv514429	chr7:83782496-83786688	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv888630	chr7:83782839-83809111	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs464	CACNA2D1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83770800-83795000	Weak transcription	NHDF-Ad	bronchial
2	chr7:83775400-83791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:83777000-83803000	Weak transcription	NHLF	lung
4	chr7:83778000-83803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:83779400-83791600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:83780000-83786600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:83780200-83786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:83783000-83788800	Weak transcription	Fetal Heart	heart
9	chr7:83784200-83786600	Enhancers	Rectal Smooth Muscle	rectum
10	chr7:83784200-83787200	Enhancers	Fetal Lung	lung
11	chr7:83784800-83787000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:83785000-83786600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:83785000-83789000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:83785000-83791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:83785000-83803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:83785200-83790600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:83785200-83790800	Weak transcription	Fetal Stomach	stomach
18	chr7:83785800-83786600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:83786200-83786600	Enhancers	Colon Smooth Muscle	Colon
20	chr7:83786200-83787200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr7:83786400-83787000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:83786400-83787000	Enhancers	NH-A	brain
23	chr7:83786400-83787200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:83786400-83787200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr7:83786400-83787200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:83786400-83787400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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