Variant report

Variant	rs16890716
Chromosome Location	chr6:80131140-80131141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGRL2-2	chr6:80130755-80131186	NONHSAT113689
2	lnc-SH3BGRL2-2	chr6:80130758-80131144	NONHSAT113690

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10484943	0.84[ASN][1000 genomes]
rs1385530	0.82[ASN][1000 genomes]
rs16890720	0.82[ASN][1000 genomes]
rs174525	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17726405	0.84[ASN][1000 genomes]
rs17726513	1.00[ASN][1000 genomes]
rs17743065	0.82[ASN][1000 genomes]
rs17743190	0.82[ASN][1000 genomes]
rs17799462	0.82[ASN][1000 genomes]
rs17799708	0.82[ASN][1000 genomes]
rs17799762	0.82[ASN][1000 genomes]
rs17799805	0.82[ASN][1000 genomes]
rs17800074	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs196667	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs196670	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846735	0.82[ASN][1000 genomes]
rs3857449	0.82[ASN][1000 genomes]
rs3857450	0.82[ASN][1000 genomes]
rs3857451	0.82[ASN][1000 genomes]
rs3857453	0.82[ASN][1000 genomes]
rs3857454	0.82[ASN][1000 genomes]
rs3907327	0.82[ASN][1000 genomes]
rs3907328	0.82[ASN][1000 genomes]
rs3907329	0.82[ASN][1000 genomes]
rs4364439	0.82[ASN][1000 genomes]
rs4580824	0.91[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55715962	0.82[ASN][1000 genomes]
rs55805600	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56226127	0.82[ASN][1000 genomes]
rs56277073	0.82[ASN][1000 genomes]
rs62411314	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62411317	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925847	0.84[ASN][1000 genomes]
rs6939506	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1030126	chr6:80113449-80209165	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16890716	IMPG1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80116200-80131600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:80123600-80131800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:80126400-80131400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:80129800-80131200	Enhancers	NHLF	lung
5	chr6:80129800-80131600	Enhancers	HUVEC	blood vessel
6	chr6:80129800-80133200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:80130000-80131200	Enhancers	Fetal Muscle Leg	muscle
8	chr6:80130000-80131600	Enhancers	HSMMtube	muscle
9	chr6:80130000-80132200	Enhancers	Fetal Lung	lung
10	chr6:80130200-80131200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:80130200-80131200	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr6:80130200-80131200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:80130200-80131600	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:80130200-80132400	Enhancers	Osteobl	bone
15	chr6:80130400-80131600	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr6:80130400-80132000	Enhancers	Fetal Intestine Large	intestine
17	chr6:80130400-80132200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:80130600-80131200	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr6:80130600-80131200	Enhancers	NHDF-Ad	bronchial
20	chr6:80130600-80131400	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr6:80130600-80131800	Enhancers	Fetal Brain Male	brain
22	chr6:80130600-80132000	Enhancers	Dnd41	blood
23	chr6:80130600-80132400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:80130600-80132600	Enhancers	Hela-S3	cervix
25	chr6:80130800-80131200	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr6:80130800-80131200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:80130800-80131200	Enhancers	NH-A	brain
28	chr6:80130800-80132000	Enhancers	Fetal Stomach	stomach
29	chr6:80130800-80132200	Enhancers	Fetal Heart	heart
30	chr6:80130800-80132400	Enhancers	Brain Germinal Matrix	brain
31	chr6:80130800-80132600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:80131000-80131200	Active TSS	Brain Hippocampus Middle	brain
33	chr6:80131000-80131200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:80131000-80131600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:80131000-80131600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:80131000-80131600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:80131000-80132400	Enhancers	HSMM	muscle

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