Variant report

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10512061	0.80[JPT][hapmap]
rs10735649	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10746998	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10746999	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10781372	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10781373	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10869809	0.80[AMR][1000 genomes]
rs1536820	0.80[JPT][hapmap]
rs4744804	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4745572	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488165	0.90[JPT][hapmap]
rs491798	0.80[ASN][1000 genomes]
rs519983	0.90[JPT][hapmap]
rs530978	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs551262	0.90[JPT][hapmap]
rs557352	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs571960	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs620985	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs630423	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs659003	0.80[ASN][1000 genomes]
rs670879	0.83[CHB][hapmap]
rs684639	0.88[JPT][hapmap]
rs685011	0.90[JPT][hapmap]
rs7866240	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4744803	KIAA0367	cis	multi-tissue	Pritchard
rs4744803	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
2	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
3	chr9:79330400-79333600	Enhancers	Rectal Smooth Muscle	rectum
4	chr9:79330400-79334000	Enhancers	Brain Hippocampus Middle	brain
5	chr9:79331000-79333600	Enhancers	HSMMtube	muscle
6	chr9:79331000-79333800	Enhancers	Brain Cingulate Gyrus	brain
7	chr9:79331000-79334000	Enhancers	Brain Substantia Nigra	brain
8	chr9:79331200-79333600	Enhancers	Osteobl	bone
9	chr9:79331600-79333800	Enhancers	Colon Smooth Muscle	Colon
10	chr9:79332000-79333800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:79332600-79333600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr9:79333000-79333600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:79333000-79340000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:79333200-79334000	Genic enhancers	HSMM	muscle
15	chr9:79333200-79338200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:79333200-79346800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:79333200-79359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--

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