Variant report

Variant	rs3088106
Chromosome Location	chr4:781098-781099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:779184..781836-chr4:815756..818416,2	MCF-7	breast:
2	chr1:166940001..166941556-chr4:781082..783860,2	MCF-7	breast:
3	chr4:780193..782237-chr4:884092..886057,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCGF3-1	chr4:781030-781654	NONHSAT094620

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13108435	0.84[AFR][1000 genomes]
rs13111051	0.82[AFR][1000 genomes]
rs13130087	0.84[AFR][1000 genomes]
rs13149773	0.82[AFR][1000 genomes]
rs28638011	0.82[AFR][1000 genomes]
rs3733356	0.82[AFR][1000 genomes]
rs3733357	0.81[AFR][1000 genomes]
rs3775137	0.82[AFR][1000 genomes]
rs3775138	0.84[AFR][1000 genomes]
rs3775139	0.84[AFR][1000 genomes]
rs3775140	0.84[AFR][1000 genomes]
rs3775141	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775142	0.81[AMR][1000 genomes]
rs3816675	0.82[AFR][1000 genomes]
rs3816677	0.82[AFR][1000 genomes]
rs3816683	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822027	0.82[AFR][1000 genomes]
rs6815765	0.81[AFR][1000 genomes]
rs6816792	0.86[AFR][1000 genomes]
rs6816868	0.81[AFR][1000 genomes]
rs6838243	0.82[AFR][1000 genomes]
rs6850266	0.84[AFR][1000 genomes]
rs7655749	0.82[AFR][1000 genomes]
rs7655941	0.82[AFR][1000 genomes]
rs7661962	0.82[AFR][1000 genomes]
rs7674850	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription 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	104 gene(s)	inside rSNPs	diseases
9	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv818207	chr4:753944-821490	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
17	nsv878261	chr4:756686-1047794	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv1007928	chr4:757263-813885	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv1003219	chr4:769894-1105464	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
20	nsv526780	chr4:771587-786401	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv521402	chr4:771587-793763	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv878262	chr4:771587-865227	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
23	nsv878263	chr4:771587-1047794	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
24	nsv964736	chr4:777089-807477	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3088106	RP11-440L14.1	cis	Esophagus Muscularis	GTEx
rs3088106	RP11-440L14.1	cis	Whole Blood	GTEx
rs3088106	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:777800-781800	Weak transcription	Liver	Liver
2	chr4:778400-781200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr4:778600-784800	Bivalent Enhancer	Fetal Thymus	thymus
4	chr4:778800-781400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:779000-781400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:779000-781400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:779800-781200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
8	chr4:780200-781200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:780200-781400	Bivalent Enhancer	Fetal Intestine Large	intestine
10	chr4:780200-781800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:780400-781200	Enhancers	Gastric	stomach
12	chr4:780400-781400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr4:780400-781800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr4:780400-781800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr4:780400-781800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr4:780400-784800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr4:780600-781200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr4:780600-781200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr4:780600-781200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:780600-781200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
21	chr4:780600-781400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr4:780600-781800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:780800-781200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
24	chr4:780800-781200	Bivalent Enhancer	Fetal Lung	lung
25	chr4:780800-781200	Enhancers	Right Ventricle	heart
26	chr4:780800-781200	Bivalent Enhancer	HUVEC	blood vessel
27	chr4:780800-781400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
28	chr4:780800-781400	Bivalent Enhancer	Spleen	Spleen
29	chr4:780800-781600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
30	chr4:780800-781800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr4:780800-781800	Enhancers	Ovary	ovary
32	chr4:780800-782000	Enhancers	GM12878-XiMat	blood
33	chr4:780800-788800	Weak transcription	Right Atrium	heart
34	chr4:781000-781200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:781000-781200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:781000-781200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:781000-781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:781000-781200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:781000-781200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:781000-781200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
41	chr4:781000-781200	Flanking Active TSS	Left Ventricle	heart
42	chr4:781000-781200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr4:781000-781800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
44	chr4:781000-781800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:781000-782800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:781000-786000	Weak transcription	Pancreas	Pancrea

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