Variant report

Variant	rs484299
Chromosome Location	chr1:77098729-77098730
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1173686	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1184626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341023	0.81[ASN][1000 genomes]
rs341025	0.81[JPT][hapmap]
rs341026	0.93[ASN][1000 genomes]
rs550021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563768	0.80[ASN][1000 genomes]
rs564853	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs587021	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs601818	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs604078	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs608880	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs621590	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628482	0.83[ASN][1000 genomes]
rs636038	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657522	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs657871	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs658026	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs658035	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs673048	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs674836	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs676269	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.91[ASN][1000 genomes]
rs677158	0.82[ASN][1000 genomes]
rs680970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683148	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687569	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs689423	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv526433	chr1:77030764-77268215	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv508315	chr1:77040085-77134730	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1001253	chr1:77077660-77234093	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs484299	ASB17	cis	cerebellum	SCAN
rs484299	ZIK1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77090000-77099000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:77097800-77099400	Enhancers	Primary T cells from cord blood	blood
3	chr1:77098000-77098800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:77098000-77098800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:77098200-77098800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:77098400-77098800	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:77098400-77099000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:77098400-77099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:77098600-77099000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:77098600-77106200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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