Variant report

Variant	rs9868898
Chromosome Location	chr3:111480946-111480947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs13317985	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13321524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13322494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13325336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs28479130	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28534728	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28648833	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4075549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4276156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4390898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4542994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4634085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56005252	0.91[ASN][1000 genomes]
rs56052712	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56215064	0.81[EUR][1000 genomes]
rs57902958	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58124137	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58663746	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60867472	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66786213	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66856712	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66975684	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6762572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6778818	1.00[CHB][hapmap]
rs6782513	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6787278	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6789977	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6798476	0.82[JPT][hapmap]
rs6800047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800065	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800922	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73222475	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73222477	0.83[ASN][1000 genomes]
rs73222500	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7614433	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs7627909	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs9842396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9843288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9858064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858228	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9862472	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9871034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9877777	0.81[EUR][1000 genomes]
rs9880633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9868898	VWA5B1	cis	Liver	GTEx
rs9868898	EN2	cis	Liver	GTEx
rs9868898	DAZ3	trans	multi-tissue	Pritchard
rs9868898	TMPRSS7	cis	parietal	SCAN
rs9868898	DRD3	trans	multi-tissue	Pritchard
rs9868898	DRD3	cis	Liver	GTEx
rs9868898	HSS00082987	trans	multi-tissue	Pritchard
rs9868898	DLK1	cis	Liver	GTEx
rs9868898	DAZ3	cis	Liver	GTEx
rs9868898	TMPRSS7	cis	cerebellum	SCAN
rs9868898	IL1F9	cis	Liver	GTEx
rs9868898	OR4K7P	cis	Liver	GTEx
rs9868898	ENST00000270920	trans	multi-tissue	Pritchard
rs9868898	GNL3L	cis	Liver	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111477400-111481800	Weak transcription	Left Ventricle	heart
2	chr3:111477600-111484600	Enhancers	HMEC	breast
3	chr3:111478000-111484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:111478800-111484200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:111478800-111484200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:111478800-111484800	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:111479200-111482600	Weak transcription	HepG2	liver
8	chr3:111479800-111481000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:111479800-111481000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:111479800-111481000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:111479800-111481000	Enhancers	Aorta	Aorta
12	chr3:111479800-111483800	Enhancers	A549	lung
13	chr3:111479800-111484400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:111479800-111484800	Enhancers	Osteobl	bone
15	chr3:111480000-111484000	Enhancers	NH-A	brain
16	chr3:111480000-111484400	Enhancers	Colon Smooth Muscle	Colon
17	chr3:111480000-111484400	Enhancers	Hela-S3	cervix
18	chr3:111480200-111481000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr3:111480200-111481400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:111480200-111481600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:111480200-111482000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:111480200-111484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:111480200-111484400	Enhancers	NHLF	lung
24	chr3:111480200-111484600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:111480200-111492000	Enhancers	Liver	Liver
26	chr3:111480400-111482200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr3:111480400-111482200	Enhancers	Fetal Thymus	thymus
28	chr3:111480400-111482800	Enhancers	Fetal Muscle Leg	muscle
29	chr3:111480400-111483000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:111480400-111483000	Enhancers	Fetal Stomach	stomach
31	chr3:111480400-111484400	Enhancers	NHEK	skin
32	chr3:111480600-111481000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:111480600-111481000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:111480600-111483000	Weak transcription	Fetal Lung	lung
35	chr3:111480600-111484200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:111480600-111484400	Enhancers	HSMMtube	muscle
37	chr3:111480600-111484800	Enhancers	NHDF-Ad	bronchial
38	chr3:111480600-111486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:111480800-111481000	Enhancers	Right Atrium	heart
40	chr3:111480800-111481000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:111480800-111481200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:111480800-111481200	Weak transcription	Fetal Heart	heart
43	chr3:111480800-111481200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:111480800-111481800	Weak transcription	Stomach Mucosa	stomach
45	chr3:111480800-111482000	Enhancers	Esophagus	oesophagus
46	chr3:111480800-111483400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:111480800-111483400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:111480800-111484200	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:111480800-111484400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:111480800-111484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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