Variant report

Variant	rs58781679
Chromosome Location	chr5:179721164-179721165
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	CTCF	chr5:179720085-179721305	SK-N-SH	brain:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
2	POLR2A	chr5:179720865-179721176	HepG2	liver:	n/a	n/a
3	CTCF	chr5:179720039-179721448	A549	lung:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698

No.	Distal block	Cell Line	Cell type
1	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
2	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:
3	chr5:179720435..179721221-chr5:179897609..179898164,2	MCF-7	breast:
4	chr5:179720624..179723530-chr5:179725711..179728473,2	K562	blood:
5	chr2:178298391..178298891-chr5:179720979..179721480,2	Hela-S3	cervix:
6	chr5:179720249..179721437-chr5:179755481..179756336,5	K562	blood:
7	chr5:179720392..179721373-chr5:179895885..179896410,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNOT6-4	chr5:179719184-179722539	NONHSAT105673

Variant related genes	Relation type
MAPK9	TF binding region
ENSG00000113300	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs34147472	1.00[AMR][1000 genomes]
rs34461510	1.00[AMR][1000 genomes]
rs34808895	1.00[AMR][1000 genomes]
rs35089249	1.00[AMR][1000 genomes]
rs35106284	1.00[AMR][1000 genomes]
rs35288370	1.00[AMR][1000 genomes]
rs35568530	1.00[AMR][1000 genomes]
rs35765078	1.00[AMR][1000 genomes]
rs35782688	1.00[AMR][1000 genomes]
rs35886948	1.00[AMR][1000 genomes]
rs36052878	1.00[AMR][1000 genomes]
rs58748693	1.00[AMR][1000 genomes]
rs58779877	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61519718	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
9	esv3398259	chr5:179717146-179721444	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720000-179721800	Enhancers	Gastric	stomach
2	chr5:179720000-179722800	Weak transcription	HSMMtube	muscle
3	chr5:179720000-179727400	Weak transcription	Ovary	ovary
4	chr5:179720400-179721800	Enhancers	Placenta	Placenta
5	chr5:179720400-179722200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr5:179720400-179722200	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:179720600-179721200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:179720600-179721200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:179720600-179721200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:179720600-179721200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr5:179720600-179721200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr5:179720600-179721200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:179720600-179721200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr5:179720600-179721200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr5:179720600-179721200	Enhancers	A549	lung
16	chr5:179720600-179721400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:179720600-179721400	Weak transcription	Fetal Stomach	stomach
18	chr5:179720600-179721600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:179720600-179721600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr5:179720600-179721800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:179720600-179722000	Enhancers	Primary B cells from cord blood	blood
22	chr5:179720600-179722200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:179720600-179722200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:179720600-179722200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr5:179720600-179722200	Enhancers	K562	blood
26	chr5:179720600-179722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:179720600-179722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:179720600-179722400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells	blood
30	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:179720600-179722600	Weak transcription	Brain Germinal Matrix	brain
32	chr5:179720600-179722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:179720600-179722800	Weak transcription	Colonic Mucosa	Colon
34	chr5:179720600-179723000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:179720600-179723200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:179720600-179723200	Weak transcription	Fetal Intestine Large	intestine
37	chr5:179720600-179724800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:179720600-179725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:179720600-179726800	Weak transcription	Osteobl	bone
40	chr5:179720600-179727200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:179720600-179727200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:179720600-179727200	Weak transcription	HSMM	muscle
43	chr5:179720600-179727400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:179720600-179727400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:179720600-179727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:179720600-179727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:179720600-179727600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:179720600-179727600	Weak transcription	NH-A	brain
49	chr5:179720600-179727800	Weak transcription	Aorta	Aorta
50	chr5:179720600-179727800	Weak transcription	Lung	lung

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