Variant report

Variant	rs6487099
Chromosome Location	chr12:20660133-20660134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11045273	1.00[CHB][hapmap]
rs11613220	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12832108	0.90[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4762764	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4762968	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4762973	0.91[EUR][1000 genomes]
rs7134968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7303852	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7484304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs7487227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7489188	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953905	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7977362	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6487099	DGCR5	trans	parietal	SCAN
rs6487099	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20647000-20660600	Weak transcription	Left Ventricle	heart
2	chr12:20647200-20664000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:20648200-20660800	Weak transcription	Aorta	Aorta
4	chr12:20649600-20660600	Weak transcription	Right Ventricle	heart
5	chr12:20649600-20662000	Weak transcription	Pancreas	Pancrea
6	chr12:20652800-20660200	Weak transcription	HUVEC	blood vessel
7	chr12:20656800-20660600	Enhancers	A549	lung
8	chr12:20658200-20660600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:20658400-20660200	Weak transcription	Fetal Heart	heart
10	chr12:20658600-20660200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:20658600-20660200	Weak transcription	Osteobl	bone
12	chr12:20658600-20660400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:20658600-20660600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:20658800-20660400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:20658800-20660400	Weak transcription	NHDF-Ad	bronchial
16	chr12:20659000-20660400	Weak transcription	NHLF	lung
17	chr12:20659400-20660200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:20659600-20661000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:20659800-20660800	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:20660000-20660800	Strong transcription	Fetal Intestine Large	intestine
21	chr12:20660000-20660800	Enhancers	Stomach Smooth Muscle	stomach
22	chr12:20660000-20661000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:20660000-20661200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:20660000-20661200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:20660000-20661400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:20660000-20665000	Strong transcription	Hela-S3	cervix

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