Variant report

Variant	rs1934931
Chromosome Location	chr9:18546968-18546969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10732338	0.87[EUR][1000 genomes]
rs10810975	0.92[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs10963623	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs10963629	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963630	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10963636	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10963642	0.96[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12336626	0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs13300724	0.97[ASN][1000 genomes]
rs13301259	0.88[CHB][hapmap]
rs1341058	0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1341060	0.89[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1361534	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1417641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1928534	0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1934932	0.83[EUR][1000 genomes]
rs2383074	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2383075	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961657	0.80[ASN][1000 genomes]
rs4961658	0.85[ASN][1000 genomes]
rs6475225	0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6475227	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475230	0.88[CEU][hapmap]
rs6475232	0.80[GIH][hapmap];0.81[TSI][hapmap]
rs7018651	0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7027141	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs7036067	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7041523	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7044243	0.84[ASN][1000 genomes]
rs7390426	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7863071	0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7867817	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7872574	0.89[ASN][1000 genomes]
rs9792478	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv892690	chr9:18485434-18592374	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv428536	chr9:18512807-18667760	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	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
12	nsv892693	chr9:18541710-18584860	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1934931	CDKN2A	cis	cerebellum	SCAN
rs1934931	KIAA1797	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18544400-18547400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:18544600-18548200	Weak transcription	Fetal Stomach	stomach
3	chr9:18544600-18554800	Weak transcription	HUVEC	blood vessel
4	chr9:18546000-18549800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:18546000-18550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:18546200-18547400	Strong transcription	HSMM	muscle
7	chr9:18546200-18564600	Weak transcription	NH-A	brain
8	chr9:18546200-18574000	Weak transcription	Fetal Heart	heart
9	chr9:18546400-18547200	Weak transcription	NHDF-Ad	bronchial
10	chr9:18546400-18555600	Weak transcription	Fetal Kidney	kidney
11	chr9:18546400-18557200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:18546600-18547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:18546600-18553600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:18546800-18547600	Weak transcription	Osteobl	bone
15	chr9:18546800-18549600	Weak transcription	Muscle Satellite Cultured Cells	--

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