Variant report

Variant	rs9289650
Chromosome Location	chr3:142467767-142467768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10049098	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10049364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10935469	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12330897	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs12330901	1.00[AMR][1000 genomes]
rs13320613	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322816	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13325615	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13434361	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16834067	1.00[AMR][1000 genomes]
rs16852648	1.00[AMR][1000 genomes]
rs16852649	1.00[AMR][1000 genomes]
rs16852658	1.00[AMR][1000 genomes]
rs1916641	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28373594	1.00[AMR][1000 genomes]
rs28460347	1.00[AMR][1000 genomes]
rs28505293	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28564963	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28572271	1.00[AMR][1000 genomes]
rs28678273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28728040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58015805	1.00[AMR][1000 genomes]
rs6798447	1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72988625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990716	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992624	1.00[AMR][1000 genomes]
rs72992644	1.00[AMR][1000 genomes]
rs72992647	1.00[AMR][1000 genomes]
rs72992650	1.00[AMR][1000 genomes]
rs73002086	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73002087	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7622773	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7637053	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638554	0.98[AFR][1000 genomes]
rs7641418	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809475	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810360	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810606	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811051	0.84[AFR][1000 genomes]
rs9819681	1.00[AMR][1000 genomes]
rs9823492	0.94[YRI][hapmap]
rs9826191	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827373	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836232	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9837730	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9839771	1.00[AMR][1000 genomes]
rs9846572	1.00[AMR][1000 genomes]
rs9847616	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850432	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863330	1.00[AMR][1000 genomes]
rs9867286	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9867886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9875489	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9877174	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877670	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879367	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882985	0.86[AFR][1000 genomes];1.00[AMR][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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:142445000-142467800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
4	chr3:142452800-142489000	Weak transcription	Aorta	Aorta
5	chr3:142458000-142482800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:142459000-142470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:142461800-142470600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:142462000-142467800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:142464800-142493200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:142465000-142469000	Weak transcription	K562	blood
11	chr3:142465400-142468000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:142465600-142471800	Weak transcription	HepG2	liver
13	chr3:142466000-142469600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:142466000-142488400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:142466200-142474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:142466400-142467800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:142466400-142478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:142466400-142479000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:142467000-142468400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:142467000-142468400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:142467000-142468400	Strong transcription	A549	lung
22	chr3:142467000-142468400	Strong transcription	NHDF-Ad	bronchial
23	chr3:142467000-142468400	Strong transcription	Osteobl	bone
24	chr3:142467000-142469800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:142467200-142467800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:142467200-142467800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:142467200-142467800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:142467200-142468000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:142467200-142468200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:142467200-142468400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:142467200-142468400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:142467200-142468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:142467200-142468400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:142467200-142468400	Strong transcription	Left Ventricle	heart
35	chr3:142467200-142468400	Strong transcription	NH-A	brain
36	chr3:142467200-142468600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:142467200-142468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:142467200-142468800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:142467200-142468800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:142467200-142469200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:142467200-142469600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:142467200-142470600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:142467400-142468000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr3:142467400-142468200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr3:142467400-142468200	Strong transcription	Brain Anterior Caudate	brain
46	chr3:142467400-142468200	Strong transcription	Fetal Brain Male	brain
47	chr3:142467400-142468200	Strong transcription	Ovary	ovary
48	chr3:142467400-142468400	Strong transcription	HMEC	breast
49	chr3:142467400-142468400	Strong transcription	HSMM	muscle
50	chr3:142467400-142468600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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