Variant report

Variant	rs1469057
Chromosome Location	chr5:179720981-179720982
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	ESRRA	chr5:179720110-179721035	GM12878	blood:	n/a	chr5:179720583-179720595
2	MAZ	chr5:179717708-179721036	IMR90	lung:	n/a	chr5:179719295-179719302 chr5:179718302-179718312
3	CTCF	chr5:179720179-179721094	HCT-116	colon:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
4	RAD21	chr5:179720306-179720985	A549	lung:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
5	MAX	chr5:179720436-179720981	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr5:179720247-179721115	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr5:179720960-179721110	HAc	cerebellar:	n/a	n/a
8	RAD21	chr5:179720326-179720988	H1-hESC	embryonic stem cell:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
9	MAX	chr5:179720103-179721008	A549	lung:	n/a	n/a
10	CTCF	chr5:179720040-179721159	HCT-116	colon:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
11	TCF12	chr5:179719977-179721065	A549	lung:	n/a	n/a
12	CTCF	chr5:179720085-179721305	SK-N-SH	brain:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
13	POLR2A	chr5:179720010-179721145	SK-N-MC	brain:	n/a	n/a
14	JUN	chr5:179720038-179720984	K562	blood:	n/a	chr5:179720162-179720171
15	ZEB1	chr5:179720476-179721038	GM12878	blood:	n/a	chr5:179720768-179720777 chr5:179720791-179720798 chr5:179720789-179720798
16	SMC3	chr5:179720097-179721059	SK-N-SH	brain:	n/a	chr5:179720683-179720697 chr5:179720683-179720690
17	RAD21	chr5:179720388-179720984	IMR90	lung:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
18	POLR2A	chr5:179720865-179721176	HepG2	liver:	n/a	n/a
19	BCL3	chr5:179720340-179721023	A549	lung:	n/a	n/a
20	RAD21	chr5:179720112-179721103	HCT-116	colon:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
21	MAX	chr5:179720400-179720983	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZEB1	chr5:179720626-179720986	GM12878	blood:	n/a	chr5:179720768-179720777 chr5:179720791-179720798 chr5:179720789-179720798
23	CTCF	chr5:179720039-179721448	A549	lung:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
24	RAD21	chr5:179720081-179721093	SK-N-SH	brain:	n/a	chr5:179720682-179720701 chr5:179720796-179720806

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	chr5:179628129..179628639-chr5:179720355..179721073,2	MCF-7	breast:
5	chr5:179720624..179723530-chr5:179725711..179728473,2	K562	blood:
6	chr5:179720585..179721111-chr5:179742335..179742892,2	K562	blood:
7	chr2:178298391..178298891-chr5:179720979..179721480,2	Hela-S3	cervix:
8	chr5:179720287..179721046-chr5:179740621..179741577,2	MCF-7	breast:
9	chr5:179720249..179721437-chr5:179755481..179756336,5	K562	blood:
10	chr5:179720392..179721373-chr5:179895885..179896410,2	MCF-7	breast:
11	chr5:179720303..179721088-chr5:179756913..179757480,2	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: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10055178	0.89[EUR][1000 genomes]
rs11949992	0.91[EUR][1000 genomes]
rs12516726	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12519634	0.95[ASN][1000 genomes]
rs13154847	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179475	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4235510	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290978	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4425468	0.84[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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179718200-179721000	Active TSS	Fetal Kidney	kidney
2	chr5:179720000-179721000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:179720000-179721000	Enhancers	Fetal Muscle Trunk	muscle
4	chr5:179720000-179721000	Enhancers	Small Intestine	intestine
5	chr5:179720000-179721000	Enhancers	Stomach Mucosa	stomach
6	chr5:179720000-179721000	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr5:179720000-179721800	Enhancers	Gastric	stomach
8	chr5:179720000-179722800	Weak transcription	HSMMtube	muscle
9	chr5:179720000-179727400	Weak transcription	Ovary	ovary
10	chr5:179720400-179721000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:179720400-179721000	Enhancers	Esophagus	oesophagus
12	chr5:179720400-179721000	Enhancers	Fetal Brain Male	brain
13	chr5:179720400-179721000	Enhancers	Fetal Thymus	thymus
14	chr5:179720400-179721800	Enhancers	Placenta	Placenta
15	chr5:179720400-179722200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr5:179720400-179722200	Enhancers	Primary B cells from peripheral blood	blood
17	chr5:179720600-179721000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179720600-179721000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:179720600-179721000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:179720600-179721000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:179720600-179721000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:179720600-179721000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:179720600-179721000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:179720600-179721000	Enhancers	Adipose Nuclei	Adipose
25	chr5:179720600-179721000	Enhancers	Brain Anterior Caudate	brain
26	chr5:179720600-179721000	Enhancers	Brain Hippocampus Middle	brain
27	chr5:179720600-179721000	Enhancers	Colon Smooth Muscle	Colon
28	chr5:179720600-179721000	Enhancers	Fetal Muscle Leg	muscle
29	chr5:179720600-179721000	Enhancers	Pancreas	Pancrea
30	chr5:179720600-179721000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:179720600-179721000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr5:179720600-179721000	Enhancers	GM12878-XiMat	blood
33	chr5:179720600-179721000	Enhancers	Hela-S3	cervix
34	chr5:179720600-179721200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr5:179720600-179721200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr5:179720600-179721200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:179720600-179721200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr5:179720600-179721200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:179720600-179721200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:179720600-179721200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr5:179720600-179721200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr5:179720600-179721200	Enhancers	A549	lung
43	chr5:179720600-179721400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr5:179720600-179721400	Weak transcription	Fetal Stomach	stomach
45	chr5:179720600-179721600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr5:179720600-179721600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr5:179720600-179721800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr5:179720600-179722000	Enhancers	Primary B cells from cord blood	blood
49	chr5:179720600-179722200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:179720600-179722200	Enhancers	Primary monocytes fromperipheralblood	blood

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