Variant report

Variant	rs1604
Chromosome Location	chr3:142468346-142468347
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11715459	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11915805	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1382688	0.92[ASN][1000 genomes]
rs1871349	0.83[ASN][1000 genomes]
rs2033912	0.92[ASN][1000 genomes]
rs2177398	0.92[ASN][1000 genomes]
rs28571594	0.89[AMR][1000 genomes]
rs28689551	0.92[ASN][1000 genomes]
rs35467195	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35862982	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3844273	0.82[ASN][1000 genomes]
rs4539980	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4643748	0.91[ASN][1000 genomes]
rs55722917	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56775607	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59108985	0.92[ASN][1000 genomes]
rs6440104	0.86[AMR][1000 genomes]
rs6440106	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6440107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440108	0.92[ASN][1000 genomes]
rs6440110	0.90[ASN][1000 genomes]
rs6772222	0.92[ASN][1000 genomes]
rs6784998	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803681	0.89[ASN][1000 genomes]
rs7621642	0.92[ASN][1000 genomes]
rs7623762	0.89[AMR][1000 genomes]
rs7626908	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629129	0.85[AMR][1000 genomes]
rs7638459	0.92[ASN][1000 genomes]
rs7639403	0.92[ASN][1000 genomes]
rs7644704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653309	0.92[ASN][1000 genomes]
rs953239	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9754885	0.80[ASN][1000 genomes]
rs9820721	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823836	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9824476	0.92[ASN][1000 genomes]
rs9835135	0.91[ASN][1000 genomes]
rs9836269	0.92[ASN][1000 genomes]
rs9849461	0.88[ASN][1000 genomes]
rs9861598	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864230	0.92[ASN][1000 genomes]
rs9865053	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][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	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
3	chr3:142452800-142489000	Weak transcription	Aorta	Aorta
4	chr3:142458000-142482800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:142459000-142470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:142461800-142470600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:142464800-142493200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:142465000-142469000	Weak transcription	K562	blood
9	chr3:142465600-142471800	Weak transcription	HepG2	liver
10	chr3:142466000-142469600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:142466000-142488400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:142466200-142474400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:142466400-142478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:142466400-142479000	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:142467000-142468400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:142467000-142468400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:142467000-142468400	Strong transcription	A549	lung
18	chr3:142467000-142468400	Strong transcription	NHDF-Ad	bronchial
19	chr3:142467000-142468400	Strong transcription	Osteobl	bone
20	chr3:142467000-142469800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:142467200-142468400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:142467200-142468400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:142467200-142468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:142467200-142468400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:142467200-142468400	Strong transcription	Left Ventricle	heart
26	chr3:142467200-142468400	Strong transcription	NH-A	brain
27	chr3:142467200-142468600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:142467200-142468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:142467200-142468800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:142467200-142468800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:142467200-142469200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:142467200-142469600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:142467200-142470600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:142467400-142468400	Strong transcription	HMEC	breast
35	chr3:142467400-142468400	Strong transcription	HSMM	muscle
36	chr3:142467400-142468600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:142467600-142468400	Strong transcription	Brain Germinal Matrix	brain
38	chr3:142467600-142468400	Strong transcription	Fetal Lung	lung
39	chr3:142467600-142468600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:142467600-142469600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:142467800-142468400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:142467800-142468400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:142467800-142468400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:142467800-142468400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:142467800-142503400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:142468000-142468400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:142468000-142470000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:142468000-142486800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:142468200-142468400	ZNF genes & repeats	Fetal Brain Male	brain
50	chr3:142468200-142469800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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