Variant report

Variant	rs10963919
Chromosome Location	chr9:19031231-19031232
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19029002..19031851-chr9:19047902..19050642,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10511670	0.94[CHD][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs10511671	0.82[ASW][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10811112	0.82[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10963906	0.83[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10963920	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963925	0.81[JPT][hapmap]
rs10963929	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963930	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963943	1.00[YRI][hapmap]
rs10963944	1.00[YRI][hapmap]
rs10963953	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs10963955	1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10963958	0.80[ASN][1000 genomes]
rs10963962	0.80[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10963964	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs12238548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284130	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13298563	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13302453	0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs16937267	0.87[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16937320	0.82[ASW][hapmap];0.94[CHD][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs1932451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291502	0.82[ASW][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34507853	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35804618	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36087651	0.80[ASN][1000 genomes]
rs3780221	0.80[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs7031392	0.82[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs71508775	0.80[ASN][1000 genomes]
rs71508776	0.80[ASN][1000 genomes]
rs7852850	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7865126	0.83[CHD][hapmap]

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	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS 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	8 gene(s)	inside rSNPs	diseases
2	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv892701	chr9:18999837-19032907	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv519909	chr9:19027880-19033376	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10963919	ADAMTSL1	cis	cerebellum	SCAN
rs10963919	SCARNA8	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19030400-19032200	Weak transcription	Fetal Stomach	stomach
2	chr9:19030800-19031400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:19030800-19031400	Enhancers	NHDF-Ad	bronchial
4	chr9:19031000-19031400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:19031000-19031400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:19031200-19032600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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