Variant report

Variant	rs489945
Chromosome Location	chr15:34280203-34280204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12437606	0.81[ASN][1000 genomes]
rs12442535	0.84[ASN][1000 genomes]
rs12903907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1436922	1.00[JPT][hapmap]
rs1987381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1987382	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1987383	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2551429	1.00[TSI][hapmap]
rs2632073	0.81[ASN][1000 genomes]
rs2632077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2632110	0.81[ASN][1000 genomes]
rs2684942	1.00[EUR][1000 genomes]
rs2705338	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs483279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489349	1.00[CHD][hapmap]
rs489619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519152	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520032	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520935	1.00[CHD][hapmap]
rs544003	0.85[AFR][1000 genomes]
rs568229	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640291	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs646339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685516	1.00[CHD][hapmap]
rs7163545	1.00[CHD][hapmap]
rs7175933	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs74007651	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74007652	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672432	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1044844	chr15:34065524-34296829	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv456790	chr15:34264018-34281733	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv568923	chr15:34264018-34281733	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs489945	GIMAP6	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34238000-34282400	Weak transcription	Ovary	ovary
2	chr15:34264800-34281200	Weak transcription	GM12878-XiMat	blood
3	chr15:34265200-34299600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:34265400-34294200	Weak transcription	Fetal Stomach	stomach
5	chr15:34265400-34311800	Weak transcription	Liver	Liver
6	chr15:34274400-34311000	Weak transcription	Primary B cells from cord blood	blood
7	chr15:34275400-34293200	Weak transcription	Primary T cells from cord blood	blood
8	chr15:34277400-34291200	Weak transcription	Aorta	Aorta
9	chr15:34277600-34284200	Weak transcription	Thymus	Thymus
10	chr15:34277800-34303200	Weak transcription	Gastric	stomach
11	chr15:34278000-34280400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:34278000-34280600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:34278000-34280600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:34278000-34280600	Weak transcription	NHLF	lung
15	chr15:34278200-34280600	Weak transcription	Osteobl	bone
16	chr15:34278200-34310000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:34278400-34280600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:34278400-34299600	Weak transcription	HSMM	muscle
19	chr15:34278800-34280400	Enhancers	Brain Hippocampus Middle	brain
20	chr15:34279000-34288000	Weak transcription	Fetal Intestine Small	intestine
21	chr15:34279200-34280400	Enhancers	Brain Anterior Caudate	brain
22	chr15:34279200-34281000	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:34279200-34281000	Enhancers	Brain Substantia Nigra	brain
24	chr15:34279400-34281000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr15:34279400-34281200	Enhancers	HepG2	liver
26	chr15:34279600-34280400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:34279600-34280800	Enhancers	Brain Angular Gyrus	brain
28	chr15:34279600-34280800	Enhancers	Lung	lung
29	chr15:34279600-34281000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:34279600-34281000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:34279800-34280400	Enhancers	Placenta	Placenta
32	chr15:34279800-34280800	Enhancers	Pancreas	Pancrea
33	chr15:34279800-34281000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:34280000-34280800	Enhancers	NH-A	brain
35	chr15:34280000-34281000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:34280000-34281400	Weak transcription	Spleen	Spleen
37	chr15:34280000-34282400	Weak transcription	Right Atrium	heart
38	chr15:34280200-34280400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:34280200-34280400	Enhancers	Left Ventricle	heart

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