Variant report

Variant	rs604078
Chromosome Location	chr1:77090587-77090588
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1173686	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1184626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs341023	0.83[ASN][1000 genomes]
rs341025	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs341026	0.96[ASN][1000 genomes]
rs484299	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]
rs485141	0.81[CHD][hapmap]
rs550021	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564853	0.89[ASN][1000 genomes]
rs587021	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs601818	0.88[ASN][1000 genomes]
rs608880	0.89[ASN][1000 genomes]
rs621590	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628482	0.80[ASN][1000 genomes]
rs636038	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];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs650427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657522	0.89[ASN][1000 genomes]
rs657871	0.89[ASN][1000 genomes]
rs658026	0.89[ASN][1000 genomes]
rs658035	0.89[ASN][1000 genomes]
rs673048	0.88[ASN][1000 genomes]
rs674836	0.89[ASN][1000 genomes]
rs676269	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs680970	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683148	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687569	0.89[ASN][1000 genomes]
rs689423	0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs604078	PIGK	cis	parietal	SCAN
rs604078	ZIK1	trans	parietal	SCAN
rs604078	ASB17	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77082400-77092000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:77082400-77094400	Weak transcription	Fetal Lung	lung
3	chr1:77088200-77098000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:77088800-77092000	Weak transcription	Right Atrium	heart
5	chr1:77088800-77094600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:77089800-77091000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:77089800-77094400	Weak transcription	Fetal Kidney	kidney
8	chr1:77090000-77091200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:77090000-77099000	Weak transcription	Brain Angular Gyrus	brain

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