Variant report

Variant	rs9673176
Chromosome Location	chr16:80201444-80201445
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYNLRB2-3	chr16:80201301-80201474	ENSG00000260706.1

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11150248	0.80[EUR][1000 genomes]
rs11150249	0.81[EUR][1000 genomes]
rs11640391	0.92[CEU][hapmap]
rs11640831	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11642380	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11642712	0.96[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs11646831	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11647537	0.96[EUR][1000 genomes]
rs11648337	0.95[EUR][1000 genomes]
rs11649346	0.95[EUR][1000 genomes]
rs11859592	0.87[EUR][1000 genomes]
rs11866127	0.84[EUR][1000 genomes]
rs12102804	0.83[ASN][1000 genomes]
rs12597962	0.87[EUR][1000 genomes]
rs12926031	0.87[EUR][1000 genomes]
rs12926639	0.87[EUR][1000 genomes]
rs12927541	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12927726	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12927869	0.83[EUR][1000 genomes]
rs12928265	0.84[EUR][1000 genomes]
rs12928708	0.87[EUR][1000 genomes]
rs12930060	0.83[EUR][1000 genomes]
rs1382389	0.82[EUR][1000 genomes]
rs1478504	0.92[EUR][1000 genomes]
rs16952546	0.82[ASN][1000 genomes]
rs17727704	0.87[EUR][1000 genomes]
rs17734652	0.88[EUR][1000 genomes]
rs17796688	0.86[EUR][1000 genomes]
rs1871209	0.97[ASN][1000 genomes]
rs1904184	0.94[EUR][1000 genomes]
rs1904186	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2008481	0.92[EUR][1000 genomes]
rs2061792	0.94[EUR][1000 genomes]
rs2169804	0.81[EUR][1000 genomes]
rs2169806	0.82[CHB][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs28733382	0.81[ASN][1000 genomes]
rs34149818	0.89[EUR][1000 genomes]
rs34758462	0.83[EUR][1000 genomes]
rs4300652	0.92[EUR][1000 genomes]
rs4405565	0.94[EUR][1000 genomes]
rs4889112	0.95[ASN][1000 genomes]
rs4889115	0.93[ASN][1000 genomes]
rs4889116	0.81[EUR][1000 genomes]
rs62049508	0.90[AFR][1000 genomes]
rs7189918	0.95[ASN][1000 genomes]
rs7191912	0.85[EUR][1000 genomes]
rs7193651	0.85[ASN][1000 genomes]
rs7193739	0.92[EUR][1000 genomes]
rs7201276	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7205467	0.90[ASN][1000 genomes]
rs8045772	0.86[ASN][1000 genomes]
rs8045952	0.81[ASN][1000 genomes]
rs8046518	0.93[EUR][1000 genomes]
rs8047391	0.80[EUR][1000 genomes]
rs8060188	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8060663	0.84[EUR][1000 genomes]
rs8061813	0.81[EUR][1000 genomes]
rs9673185	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930130	0.81[EUR][1000 genomes]
rs9935498	0.88[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs9935652	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9939067	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9940589	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833298	chr16:80122337-80314603	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1055982	chr16:80151604-80202923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9673176	VAT1L	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80193600-80207600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr16:80199600-80201600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:80199600-80207800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:80199800-80201600	Weak transcription	HSMM	muscle
5	chr16:80200600-80202400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr16:80200800-80201600	Enhancers	Fetal Kidney	kidney
7	chr16:80201200-80202200	Enhancers	A549	lung
8	chr16:80201400-80201800	Enhancers	Pancreas	Pancrea
9	chr16:80201400-80202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr16:80201400-80202200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr16:80201400-80202200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:80201400-80202200	Enhancers	HMEC	breast
13	chr16:80201400-80202200	Enhancers	NHEK	skin
14	chr16:80201400-80202400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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