Variant report

Variant	rs2009732
Chromosome Location	chr5:179516980-179516981
allele	A/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	ZBTB7A	chr5:179516976-179517811	ECC-1	luminal epithelium:	n/a	chr5:179517624-179517633 chr5:179517569-179517577
2	SMC3	chr5:179516946-179517915	SK-N-SH	brain:	n/a	chr5:179517477-179517487 chr5:179517625-179517639 chr5:179517625-179517635
3	ATF2	chr5:179516869-179517770	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:179516788-179517688	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr5:179516770-179516981	H1-hESC	embryonic stem cell:	n/a	chr5:179516871-179516883
6	YY1	chr5:179516662-179517645	H1-hESC	embryonic stem cell:	n/a	chr5:179516871-179516883 chr5:179517480-179517489
7	CTCF	chr5:179516960-179517110	RPTEC	kidney:	n/a	n/a
8	MAX	chr5:179516959-179517728	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr5:179516778-179517876	H1-hESC	embryonic stem cell:	n/a	chr5:179517501-179517511 chr5:179517480-179517489
10	E2F6	chr5:179516931-179517689	H1-hESC	embryonic stem cell:	n/a	chr5:179517501-179517511 chr5:179517480-179517489
11	CHD1	chr5:179516969-179517356	H1-hESC	embryonic stem cell:	n/a	n/a
12	E2F6	chr5:179516958-179517859	A549	lung:	n/a	chr5:179517501-179517511 chr5:179517480-179517489
13	CTCF	chr5:179516940-179517090	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr5:179516841-179517774	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr5:179516934-179517940	SK-N-SH	brain:	n/a	chr5:179517625-179517638 chr5:179517623-179517641 chr5:179517625-179517638 chr5:179517629-179517638 chr5:179517626-179517636 chr5:179517624-179517640 chr5:179517618-179517639
16	MAX	chr5:179516856-179517811	A549	lung:	n/a	n/a
17	CTCF	chr5:179516894-179518790	A549	lung:	n/a	chr5:179517625-179517638 chr5:179517623-179517641 chr5:179517625-179517638 chr5:179517629-179517638 chr5:179517626-179517636 chr5:179517624-179517640 chr5:179517618-179517639
18	MAX	chr5:179516912-179517784	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179451009..179454455-chr5:179516109..179519066,3	MCF-7	breast:
2	chr5:179512072..179514458-chr5:179515699..179518441,2	MCF-7	breast:
3	chr5:179104426..179106670-chr5:179516761..179519080,2	MCF-7	breast:
4	chr5:179495694..179500359-chr5:179515816..179519621,6	MCF-7	breast:
5	chr5:179497628..179501303-chr5:179515558..179519468,8	MCF-7	breast:
6	chr5:179447316..179449244-chr5:179516942..179519007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253480	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000253480	Chromatin interaction
ENSG00000225051	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10479558	0.88[AFR][1000 genomes]
rs10479559	0.88[AFR][1000 genomes]
rs1345085	0.95[AFR][1000 genomes]
rs1345088	0.97[AFR][1000 genomes]
rs6859564	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
4	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
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179509400-179517200	Weak transcription	Liver	Liver
3	chr5:179510600-179517000	Weak transcription	Fetal Brain Female	brain
4	chr5:179512600-179517000	Weak transcription	Placenta	Placenta
5	chr5:179512600-179517200	Weak transcription	Colonic Mucosa	Colon
6	chr5:179512800-179517000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179512800-179517000	Weak transcription	Brain Germinal Matrix	brain
8	chr5:179512800-179517000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:179513000-179517000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:179513000-179517000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:179513000-179517000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:179513000-179517000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:179513000-179517000	Weak transcription	Fetal Intestine Large	intestine
14	chr5:179513000-179517200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:179513000-179517200	Weak transcription	Stomach Mucosa	stomach
16	chr5:179513200-179517000	Weak transcription	Primary T cells from cord blood	blood
17	chr5:179513200-179517000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:179513200-179517000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr5:179513200-179517000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:179513200-179517000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:179513200-179517000	Weak transcription	Brain Angular Gyrus	brain
22	chr5:179513200-179517000	Weak transcription	Brain Anterior Caudate	brain
23	chr5:179513200-179517000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:179513200-179517000	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:179513200-179517000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:179513200-179517000	Weak transcription	Fetal Intestine Small	intestine
27	chr5:179513200-179517000	Weak transcription	Pancreas	Pancrea
28	chr5:179513200-179518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:179513200-179520800	Weak transcription	Spleen	Spleen
30	chr5:179513800-179517000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:179514000-179517000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:179514200-179517000	Weak transcription	Fetal Thymus	thymus
33	chr5:179514400-179517000	Weak transcription	K562	blood
34	chr5:179514800-179517000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:179515200-179517000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr5:179515200-179517000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:179515800-179517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:179516000-179517000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:179516200-179517000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:179516600-179517400	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr5:179516600-179517400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:179516600-179517800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:179516600-179517800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:179516600-179518000	Active TSS	A549	lung
45	chr5:179516800-179517000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr5:179516800-179517000	Enhancers	Primary B cells from cord blood	blood
47	chr5:179516800-179517000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr5:179516800-179517000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:179516800-179517000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:179516800-179517000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle

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