Variant report

Variant	rs12490494
Chromosome Location	chr3:158546984-158546985
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158544882..158547801-chr3:158551051..158553794,3	MCF-7	breast:
2	chr3:158541719..158543947-chr3:158545582..158547779,3	K562	blood:
3	chr3:158546388..158549031-chr3:158549491..158552747,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10513528	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12054172	0.90[ASN][1000 genomes]
rs12491877	0.84[EUR][1000 genomes]
rs13100273	0.94[ASN][1000 genomes]
rs1503099	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1503100	0.94[ASN][1000 genomes]
rs28364680	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35638572	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35961488	0.94[ASN][1000 genomes]
rs41272621	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55675199	0.87[ASN][1000 genomes]
rs55923687	0.84[ASN][1000 genomes]
rs56297607	0.82[ASN][1000 genomes]
rs61796768	0.84[EUR][1000 genomes]
rs61796770	0.84[EUR][1000 genomes]
rs61796775	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61796802	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61796815	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61796817	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73158361	0.84[EUR][1000 genomes]
rs7433816	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7652579	0.88[ASN][1000 genomes]
rs9820320	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:158527800-158554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:158528000-158547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:158528000-158549400	Weak transcription	Dnd41	blood
6	chr3:158528600-158549600	Weak transcription	Fetal Kidney	kidney
7	chr3:158528800-158547200	Weak transcription	Psoas Muscle	Psoas
8	chr3:158532200-158551800	Weak transcription	NHEK	skin
9	chr3:158532400-158557800	Weak transcription	Gastric	stomach
10	chr3:158533000-158548000	Weak transcription	Pancreas	Pancrea
11	chr3:158533000-158551000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart
14	chr3:158533200-158547600	Weak transcription	A549	lung
15	chr3:158534400-158550800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:158535400-158550600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:158535400-158551200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:158535400-158551200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:158535600-158548200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:158535600-158548600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:158535600-158550200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:158535600-158550200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:158535600-158550600	Strong transcription	Liver	Liver
24	chr3:158535600-158550800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:158535800-158548800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:158535800-158550800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr3:158536400-158548600	Strong transcription	Placenta	Placenta
28	chr3:158537400-158548600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:158537800-158550800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:158537800-158551000	Strong transcription	Adipose Nuclei	Adipose
31	chr3:158537800-158551000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:158540000-158550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:158541000-158548800	Strong transcription	Fetal Intestine Large	intestine
34	chr3:158541600-158552000	Weak transcription	Colonic Mucosa	Colon
35	chr3:158541800-158548000	Weak transcription	Aorta	Aorta
36	chr3:158541800-158551200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:158541800-158551200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:158541800-158554200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:158541800-158555000	Weak transcription	Spleen	Spleen
40	chr3:158541800-158560200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:158542000-158548200	Weak transcription	Brain Angular Gyrus	brain
42	chr3:158542000-158548800	Weak transcription	HMEC	breast
43	chr3:158542000-158556400	Weak transcription	Brain Germinal Matrix	brain
44	chr3:158542200-158547000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:158542200-158547800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:158542200-158547800	Weak transcription	Brain Anterior Caudate	brain
47	chr3:158542200-158550200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:158542200-158550200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:158542200-158552000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:158542200-158561000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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