Variant report

Variant	rs9884070
Chromosome Location	chr3:179111861-179111862
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:179111749-179111902	ProgFib	skin:	n/a	n/a
2	POLR2A	chr3:179111811-179112180	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:179111256-179111938	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:179111484-179112124	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:179111714-179112072	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:179111561-179111965	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:179111418-179112177	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr3:179111625-179112141	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:179111001-179112149	K562	blood:	n/a	n/a
10	POLR2A	chr3:179111647-179112122	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179105986..179107920-chr3:179111586..179113312,2	K562	blood:
2	chr3:179111620..179113652-chr3:179168084..179170216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242539	TF binding region
ENSG00000239255	Chromatin interaction
ENSG00000114450	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

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[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13320472	0.81[AMR][1000 genomes]
rs16830445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28512433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28522651	0.89[AMR][1000 genomes]
rs55805052	0.89[AMR][1000 genomes]
rs56265474	0.94[AFR][1000 genomes];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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59062224	0.89[AMR][1000 genomes]
rs59333548	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61325843	0.89[AMR][1000 genomes]
rs6778235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808033	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73045195	1.00[AMR][1000 genomes]
rs73045198	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[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73883508	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73883509	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73886620	0.89[AMR][1000 genomes]
rs7611533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625719	0.89[AMR][1000 genomes]
rs9814990	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9815687	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829054	1.00[AMR][1000 genomes]
rs9834493	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9861354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879952	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:124 , 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	chr3:179066800-179113600	Weak transcription	Stomach Mucosa	stomach
3	chr3:179066800-179118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
7	chr3:179081600-179113400	Weak transcription	Gastric	stomach
8	chr3:179081600-179115200	Weak transcription	Spleen	Spleen
9	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
11	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
13	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:179088600-179115400	Weak transcription	Aorta	Aorta
15	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
17	chr3:179098400-179120200	Weak transcription	Lung	lung
18	chr3:179098400-179125000	Weak transcription	Ovary	ovary
19	chr3:179099400-179119400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:179099600-179119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:179099800-179113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:179101800-179114000	Strong transcription	Liver	Liver
24	chr3:179101800-179114200	Strong transcription	Primary B cells from cord blood	blood
25	chr3:179101800-179114400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:179101800-179115800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:179101800-179119200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:179102400-179113800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:179103000-179112400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:179103000-179114400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:179103200-179120600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:179103400-179114600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:179103400-179115600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:179103400-179115600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:179103400-179115800	Strong transcription	Adipose Nuclei	Adipose
39	chr3:179103400-179115800	Strong transcription	Fetal Thymus	thymus
40	chr3:179103400-179116200	Strong transcription	HSMM	muscle
41	chr3:179103400-179116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:179103400-179119000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:179103600-179120200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:179103800-179116400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:179104000-179113200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:179104000-179113200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:179105000-179131200	Weak transcription	Fetal Heart	heart
48	chr3:179105200-179115400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:179105400-179141400	Weak transcription	Thymus	Thymus

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