Variant report

Variant	rs16830445
Chromosome Location	chr3:179133909-179133910
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179132248..179135170-chr3:179278142..179280953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136518	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11916825	0.89[AMR][1000 genomes]
rs11919840	0.89[AMR][1000 genomes]
rs11925064	0.89[AMR][1000 genomes]
rs11925248	0.89[AMR][1000 genomes]
rs11927084	0.89[AMR][1000 genomes]
rs13317510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13320472	0.81[AMR][1000 genomes]
rs16830460	0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28512433	1.00[AMR][1000 genomes]
rs28522651	0.89[AMR][1000 genomes]
rs55805052	0.89[AMR][1000 genomes]
rs56265474	1.00[AMR][1000 genomes]
rs56280435	0.89[AMR][1000 genomes]
rs57148977	0.89[AMR][1000 genomes]
rs57526364	0.89[AMR][1000 genomes]
rs57795346	0.89[AMR][1000 genomes]
rs58741861	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59062224	0.89[AMR][1000 genomes]
rs59333548	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59511701	0.89[AMR][1000 genomes]
rs59564372	0.89[AMR][1000 genomes]
rs60191176	0.89[AMR][1000 genomes]
rs60746059	0.89[AMR][1000 genomes]
rs61246771	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61325843	0.89[AMR][1000 genomes]
rs6778235	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800044	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808033	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808866	0.89[AMR][1000 genomes]
rs73043406	0.89[AMR][1000 genomes]
rs73043407	0.89[AMR][1000 genomes]
rs73043413	0.89[AMR][1000 genomes]
rs73045191	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73045195	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73045198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73059758	0.89[AMR][1000 genomes]
rs73059766	0.89[AMR][1000 genomes]
rs7355835	1.00[AMR][1000 genomes]
rs73883508	1.00[AMR][1000 genomes]
rs73883509	1.00[AMR][1000 genomes]
rs73886620	0.89[AMR][1000 genomes]
rs7611533	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618506	0.90[YRI][hapmap];0.98[AFR][1000 genomes]
rs7625719	0.89[AMR][1000 genomes]
rs9814990	1.00[AMR][1000 genomes]
rs9815687	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829054	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834493	1.00[AMR][1000 genomes]
rs9861354	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864857	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872939	0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879952	1.00[EUR][1000 genomes]
rs9884070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968068	0.89[AMR][1000 genomes]
rs9968069	0.89[AMR][1000 genomes]
rs9968075	0.89[AMR][1000 genomes]
rs9968076	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active 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 target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
3	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
4	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
7	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
10	chr3:179111600-179138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
12	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
13	chr3:179112200-179136400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:179112200-179138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
16	chr3:179112800-179144200	Weak transcription	A549	lung
17	chr3:179113800-179146800	Weak transcription	Gastric	stomach
18	chr3:179114200-179139200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:179115600-179139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:179115800-179136600	Weak transcription	Pancreas	Pancrea
21	chr3:179118000-179137600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:179120600-179138000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:179120600-179143800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:179120800-179144600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:179121000-179139400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:179121000-179149400	Weak transcription	Primary T cells from cord blood	blood
27	chr3:179121400-179143000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:179122400-179142000	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:179122600-179138200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:179122800-179149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:179123000-179143000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:179123000-179143200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:179123000-179150400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:179123200-179134600	Weak transcription	Left Ventricle	heart
35	chr3:179123200-179135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:179123200-179136400	Weak transcription	Fetal Brain Female	brain
37	chr3:179123200-179141000	Weak transcription	K562	blood
38	chr3:179123200-179141800	Weak transcription	Aorta	Aorta
39	chr3:179123200-179142200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:179123200-179154800	Weak transcription	Brain Anterior Caudate	brain
41	chr3:179123400-179134800	Weak transcription	Fetal Thymus	thymus
42	chr3:179123400-179136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:179123400-179141000	Weak transcription	Brain Germinal Matrix	brain
44	chr3:179123400-179142400	Weak transcription	Right Ventricle	heart
45	chr3:179123400-179149600	Weak transcription	Fetal Intestine Large	intestine
46	chr3:179123600-179153600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:179123800-179136200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:179123800-179156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:179124000-179141000	Weak transcription	Liver	Liver
50	chr3:179124200-179141000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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