Variant report

Variant	rs16830460
Chromosome Location	chr3:179144021-179144022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179143519..179146225-chr3:179157504..179160414,2	K562	blood:
2	chr3:179142328..179144136-chr3:179149284..179151503,2	K562	blood:

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	1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs11925064	0.89[AMR][1000 genomes]
rs11925248	1.00[MEX][hapmap];1.00[TSI][hapmap];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]
rs16830445	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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59062224	0.89[AMR][1000 genomes]
rs59333548	0.93[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61325843	0.89[AMR][1000 genomes]
rs6778235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800044	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808033	0.94[YRI][hapmap];0.93[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73045195	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73045198	0.93[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618506	1.00[YRI][hapmap];1.00[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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834493	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs9861354	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864857	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872939	1.00[YRI][hapmap];1.00[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	1.00[MEX][hapmap];1.00[TSI][hapmap];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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
2	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
3	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
6	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
7	chr3:179112800-179144200	Weak transcription	A549	lung
8	chr3:179113800-179146800	Weak transcription	Gastric	stomach
9	chr3:179120800-179144600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:179121000-179149400	Weak transcription	Primary T cells from cord blood	blood
11	chr3:179122800-179149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:179123000-179150400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:179123200-179154800	Weak transcription	Brain Anterior Caudate	brain
14	chr3:179123400-179149600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:179123600-179153600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:179123800-179156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:179127200-179145000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:179127600-179145200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:179131600-179147400	Weak transcription	Fetal Heart	heart
20	chr3:179132800-179167000	Weak transcription	Hela-S3	cervix
21	chr3:179133200-179149400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:179133400-179150400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:179137200-179149000	Weak transcription	GM12878-XiMat	blood
24	chr3:179137400-179156400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:179139200-179145000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:179139800-179149200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:179139800-179149400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:179139800-179150400	Weak transcription	Brain Substantia Nigra	brain
29	chr3:179139800-179153200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:179140400-179145200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:179140800-179144200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:179140800-179145000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:179141000-179144200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:179141000-179144200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:179141000-179144200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:179141000-179144200	Strong transcription	Dnd41	blood
37	chr3:179141000-179144200	Strong transcription	NHLF	lung
38	chr3:179141000-179144800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:179141000-179145000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:179141000-179145200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:179141000-179145200	Strong transcription	HUVEC	blood vessel
42	chr3:179141000-179145400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:179141000-179145800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:179141800-179145000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:179142000-179149400	Weak transcription	Liver	Liver
46	chr3:179142000-179149600	Weak transcription	Thymus	Thymus
47	chr3:179142200-179156400	Weak transcription	K562	blood
48	chr3:179142800-179149200	Weak transcription	Fetal Thymus	thymus
49	chr3:179143000-179144400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:179143000-179149400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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