Variant report

Variant	rs11940788
Chromosome Location	chr4:705608-705609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:703233..707351-chr4:710441..713114,3	MCF-7	breast:
2	chr4:704517..706514-chr4:717947..720061,2	K562	blood:
3	chr4:672222..675225-chr4:704052..707377,3	K562	blood:
4	chr4:697170..699923-chr4:703607..707552,5	K562	blood:

Variant related genes	Relation type
ENSG00000215375	Chromatin interaction
ENSG00000185619	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11248035	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11248036	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11734460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735280	0.81[ASN][1000 genomes]
rs12374317	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12504026	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690186	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690187	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4690188	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690292	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690293	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690294	0.82[ASN][1000 genomes]
rs4690295	0.82[ASN][1000 genomes]
rs73221103	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221104	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73221124	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	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
12	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11940788	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:701000-705800	Weak transcription	Fetal Kidney	kidney
2	chr4:701200-713400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:701200-713400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:701200-714600	Weak transcription	NHDF-Ad	bronchial
5	chr4:701200-724400	Weak transcription	Aorta	Aorta
6	chr4:701400-714000	Weak transcription	HMEC	breast
7	chr4:701400-715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:701400-724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:701400-724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:701600-716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:702200-754800	Weak transcription	Hela-S3	cervix
12	chr4:702400-708000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:702400-714600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:702400-720000	Weak transcription	Brain Substantia Nigra	brain
15	chr4:702400-720200	Weak transcription	NH-A	brain
16	chr4:702600-706000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:702600-707800	Weak transcription	NHLF	lung
18	chr4:702600-708000	Weak transcription	Colonic Mucosa	Colon
19	chr4:702600-708600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:702600-715800	Weak transcription	Liver	Liver
21	chr4:702600-716800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:702600-724400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:702800-707200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:702800-707800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:702800-708000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:702800-714600	Weak transcription	Stomach Mucosa	stomach
27	chr4:702800-715000	Weak transcription	GM12878-XiMat	blood
28	chr4:702800-726600	Weak transcription	Primary B cells from cord blood	blood
29	chr4:703000-708800	Strong transcription	Fetal Stomach	stomach
30	chr4:703000-711400	Weak transcription	Fetal Heart	heart
31	chr4:703000-714000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:703000-714000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:703000-716600	Weak transcription	Fetal Lung	lung
34	chr4:703400-708400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:703400-714400	Weak transcription	Primary T cells from cord blood	blood
36	chr4:703400-714800	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:703400-717800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:703400-724800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:703400-726800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:703600-706800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:703600-707400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:703600-708400	Weak transcription	Left Ventricle	heart
43	chr4:703600-708600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:703600-714600	Weak transcription	HUVEC	blood vessel
45	chr4:703600-727200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:703800-707600	Weak transcription	K562	blood
47	chr4:703800-715400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:703800-724400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:704000-706600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:704000-707800	Weak transcription	Adipose Nuclei	Adipose

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