Variant report

Variant	rs248230
Chromosome Location	chr5:179354082-179354083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs152232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152236	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs152237	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs152238	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs155574	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs155784	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155795	0.93[CHB][hapmap]
rs155796	0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap]
rs156096	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166032	0.80[CEU][hapmap]
rs1684973	0.93[CHB][hapmap]
rs182085	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182086	0.93[CHB][hapmap]
rs2431123	0.93[CHB][hapmap]
rs2431124	0.87[CHB][hapmap]
rs2434411	0.93[CHB][hapmap];0.80[CHD][hapmap]
rs248217	0.93[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs248218	0.93[CHB][hapmap]
rs248219	0.93[CHB][hapmap]
rs248220	0.93[CHB][hapmap]
rs248229	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248232	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248252	0.93[CHB][hapmap]
rs26074	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs26075	0.81[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26078	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27410	0.93[CHB][hapmap]
rs27411	0.93[CHB][hapmap]
rs27471	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27474	0.82[ASN][1000 genomes]
rs32437	0.93[CHB][hapmap]
rs32438	0.93[CHB][hapmap]
rs32469	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32470	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32471	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3734003	0.93[CHB][hapmap]
rs42414	0.86[JPT][hapmap]
rs43155	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs456958	0.83[CEU][hapmap]
rs457610	0.80[CEU][hapmap]
rs464219	0.80[CEU][hapmap]
rs467764	0.80[CEU][hapmap]
rs518075	0.80[CEU][hapmap]
rs532795	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs574997	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs88183	0.93[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs9957	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
3	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
5	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs248230	HIGD2A	cis	cerebellum	SCAN
rs248230	C5orf45	cis	cerebellum	SCAN
rs248230	TBC1D9B	cis	Muscle Skeletal	GTEx
rs248230	CNOT6	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179335800-179358200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:179336000-179361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:179344600-179381600	Weak transcription	Fetal Brain Male	brain
4	chr5:179347200-179381000	Weak transcription	Brain Angular Gyrus	brain
5	chr5:179347400-179358200	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:179347400-179372000	Weak transcription	Brain Germinal Matrix	brain
7	chr5:179351000-179354200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:179351000-179372200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:179351200-179354800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:179352800-179354200	Strong transcription	Fetal Brain Female	brain

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