Variant report

Variant	rs130256
Chromosome Location	chr22:32418552-32418553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32416680-32427569..22:32868055-32872511	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000100225	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12167016	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs130257	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs130264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs130268	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs130405	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13054053	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17683807	0.90[MEX][hapmap]
rs17746358	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs36065572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761432	0.93[CEU][hapmap]
rs3788440	0.93[CEU][hapmap]
rs3827334	0.93[CEU][hapmap]
rs4821026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753861	1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs6518758	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7290696	0.81[MEX][hapmap]
rs7291050	0.81[MEX][hapmap]
rs738181	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8135356	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8141732	0.81[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs933226	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9606893	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9606904	0.87[AMR][1000 genomes]
rs9606905	0.88[TSI][hapmap]
rs9606907	0.86[ASW][hapmap];0.87[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs9606908	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9609389	0.93[CEU][hapmap]
rs9609396	0.87[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs9609409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9609427	1.00[ASW][hapmap];0.87[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs9609429	0.90[MEX][hapmap]
rs9619244	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621371	0.81[MEX][hapmap]
rs9621386	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055450	chr22:32356150-32468832	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1055925	chr22:32358540-32450200	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1063876	chr22:32358540-32463271	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1061546	chr22:32358991-32464350	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1059240	chr22:32362689-32462511	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv544678	chr22:32362689-32462511	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1060529	chr22:32370432-32525699	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1063267	chr22:32379851-32462650	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv544679	chr22:32379851-32462650	Weak transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1067007	chr22:32400566-32452776	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1065893	chr22:32400566-32453047	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv834177	chr22:32416679-32594663	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs130256	ZNF292	trans	cerebellum	SCAN
rs130256	TUG1	cis	cerebellum	SCAN
rs130256	CCDC117	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32416000-32422200	Enhancers	Fetal Intestine Large	intestine
2	chr22:32416000-32422800	Enhancers	Fetal Intestine Small	intestine
3	chr22:32416800-32419200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr22:32417000-32419200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:32417000-32419200	Weak transcription	HMEC	breast
6	chr22:32417200-32421600	Enhancers	Duodenum Mucosa	Duodenum
7	chr22:32417600-32419200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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