Variant report

Variant	rs28642912
Chromosome Location	chr3:179119373-179119374
allele	C/T
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	chr3:179118935-179119431	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:179117338-179121333	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179113895..179115868-chr3:179118066..179120130,3	K562	blood:

Variant related genes	Relation type
ENSG00000269728	TF binding region
ENSG00000272699	TF binding region
ENSG00000242539	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10592	1.00[EUR][1000 genomes]
rs13313931	1.00[EUR][1000 genomes]
rs13327891	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3853150	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3853151	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3853152	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73045195	1.00[EUR][1000 genomes]
rs9816934	1.00[EUR][1000 genomes]
rs9820636	1.00[EUR][1000 genomes]
rs9821850	1.00[EUR][1000 genomes]
rs9874433	0.81[AMR][1000 genomes];1.00[EUR][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:115 , 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	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
5	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
7	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
9	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
12	chr3:179098400-179120200	Weak transcription	Lung	lung
13	chr3:179098400-179125000	Weak transcription	Ovary	ovary
14	chr3:179099400-179119400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:179099600-179119600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:179101600-179125800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:179101800-179125800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:179102200-179126400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:179103200-179120600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:179103600-179120200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:179105000-179131200	Weak transcription	Fetal Heart	heart
23	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
25	chr3:179108400-179123400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:179109400-179124600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:179110000-179123400	Strong transcription	HUVEC	blood vessel
28	chr3:179110800-179133400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:179111600-179128600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:179111600-179138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:179111800-179122400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
33	chr3:179112000-179119400	Weak transcription	Fetal Brain Female	brain
34	chr3:179112000-179122800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:179112000-179123000	Weak transcription	HepG2	liver
36	chr3:179112000-179125000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:179112000-179133000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
39	chr3:179112200-179122000	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:179112200-179136400	Weak transcription	Brain Substantia Nigra	brain
41	chr3:179112200-179138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
43	chr3:179112400-179120000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:179112400-179120000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:179112600-179122600	Weak transcription	Brain Germinal Matrix	brain
46	chr3:179112600-179122800	Weak transcription	NHLF	lung
47	chr3:179112600-179131200	Weak transcription	NHEK	skin
48	chr3:179112800-179144200	Weak transcription	A549	lung
49	chr3:179113200-179119400	Weak transcription	K562	blood
50	chr3:179113200-179122200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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