Variant report

Variant	rs72807341
Chromosome Location	chr5:179229987-179229988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179228800-179231391	K562	blood:	n/a	n/a
2	POLR2A	chr5:179229963-179231387	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:179229806-179230121	ProgFib	skin:	n/a	n/a
4	POLR2A	chr5:179229857-179230520	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:179229487-179231518	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
7	POLR2A	chr5:179229799-179230133	K562	blood:	n/a	n/a
8	CEBPB	chr5:179229927-179230039	H1-hESC	embryonic stem cell:	n/a	n/a
9	HNF4A	chr5:179229947-179230181	HepG2	liver:	n/a	chr5:179230054-179230066 chr5:179230157-179230179 chr5:179230055-179230067 chr5:179230060-179230068 chr5:179230054-179230067
10	POLR2A	chr5:179229917-179230100	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:179229668-179230519	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr5:179229886-179231742	HL-60	blood:	n/a	n/a
13	POLR2A	chr5:179229930-179230134	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr5:179229265-179230694	HepG2	liver:	n/a	n/a
15	EP300	chr5:179229348-179230616	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr5:179228473-179231388	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:179228779-179234761	K562	blood:	n/a	n/a
18	MAX	chr5:179229550-179230122	ECC-1	luminal epithelium:	n/a	n/a
19	NR2F2	chr5:179229719-179230604	MCF-7	breast:	n/a	n/a
20	NFIC	chr5:179229354-179230569	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr5:179228763-179230573	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr5:179229942-179230366	HepG2	liver:	n/a	n/a
23	POLR2A	chr5:179229954-179230280	GM12878	blood:	n/a	n/a
24	NFIC	chr5:179229454-179230575	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr5:179229426-179230114	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr5:179229521-179234618	MCF-7	breast:	n/a	n/a
27	TCF12	chr5:179229417-179230606	ECC-1	luminal epithelium:	n/a	chr5:179230022-179230032 chr5:179230429-179230436
28	POLR2A	chr5:179229692-179230033	U87	brain:	n/a	n/a
29	POLR2A	chr5:179224688-179234670	K562	blood:	n/a	n/a
30	POLR2A	chr5:179229492-179230460	Hela-S3	cervix:	n/a	n/a
31	TCF12	chr5:179229390-179230738	ECC-1	luminal epithelium:	n/a	chr5:179230022-179230032 chr5:179230429-179230436

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179158622..179161306-chr5:179229255..179232070,3	MCF-7	breast:
2	chr5:179125163..179127622-chr5:179228110..179231035,2	K562	blood:
3	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
4	chr5:179227831..179231343-chr5:179333679..179336075,3	MCF-7	breast:
5	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
6	chr5:179159678..179161359-chr5:179228559..179231556,2	MCF-7	breast:
7	chr5:179197599..179200377-chr5:179228822..179231191,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf45-4	chr5:179229313-179230030	NONHSAT105627
2	lnc-C5orf45-4	chr5:179229952-179230030	NONHSAT105628

No data

Variant related genes	Relation type
MGAT4B	TF binding region
SQSTM1	TF binding region
MIR1229	TF binding region
ENSG00000161010	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000245317	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs72807324	0.91[EUR][1000 genomes]
rs72807343	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72807345	0.82[EUR][1000 genomes]
rs72809772	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	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
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
10	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
11	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
12	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
13	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv600662	chr5:179220010-179231248	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
15	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
16	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
17	nsv883282	chr5:179220638-179231248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
18	nsv883283	chr5:179220638-179231681	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
19	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	158 gene(s)	inside rSNPs	diseases
20	nsv600665	chr5:179221789-179231248	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
21	nsv600666	chr5:179221789-179231681	Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
22	nsv883285	chr5:179223023-179238794	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	153 gene(s)	inside rSNPs	diseases
23	nsv600668	chr5:179227865-179242581	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179223800-179231600	Weak transcription	Fetal Kidney	kidney
2	chr5:179223800-179231600	Weak transcription	Psoas Muscle	Psoas
3	chr5:179224000-179230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:179224000-179230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:179224000-179230000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:179224000-179230800	Weak transcription	Right Atrium	heart
7	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:179224200-179230000	Strong transcription	Brain Germinal Matrix	brain
9	chr5:179226200-179232200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:179226800-179233200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:179227000-179230800	Weak transcription	Fetal Brain Male	brain
12	chr5:179227200-179230200	Weak transcription	HUVEC	blood vessel
13	chr5:179227200-179231000	Weak transcription	HSMMtube	muscle
14	chr5:179227200-179231800	Weak transcription	Brain Substantia Nigra	brain
15	chr5:179227400-179230200	Weak transcription	Thymus	Thymus
16	chr5:179227600-179230000	Weak transcription	Primary T cells from cord blood	blood
17	chr5:179227600-179230000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:179227600-179230000	Weak transcription	HSMM	muscle
19	chr5:179227600-179230200	Weak transcription	Fetal Lung	lung
20	chr5:179227600-179232000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr5:179227800-179232000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:179227800-179232200	Enhancers	Fetal Heart	heart
23	chr5:179228000-179230800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr5:179228000-179231200	Weak transcription	Brain Anterior Caudate	brain
25	chr5:179228000-179232400	Weak transcription	Aorta	Aorta
26	chr5:179228200-179230200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:179228400-179230000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:179228400-179230000	Weak transcription	K562	blood
29	chr5:179228400-179231000	Genic enhancers	Rectal Mucosa Donor 29	rectum
30	chr5:179228400-179232400	Genic enhancers	Placenta	Placenta
31	chr5:179228600-179230000	Weak transcription	Dnd41	blood
32	chr5:179228600-179230200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:179228600-179230800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:179228600-179230800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:179228600-179230800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr5:179228600-179230800	Weak transcription	Small Intestine	intestine
37	chr5:179228600-179231000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:179228600-179231200	Weak transcription	Ovary	ovary
39	chr5:179228600-179231400	Weak transcription	Fetal Brain Female	brain
40	chr5:179228600-179232200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:179228800-179230000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:179228800-179230000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:179228800-179230000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:179228800-179230000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:179228800-179230000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr5:179228800-179230200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:179228800-179230400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr5:179228800-179230400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:179228800-179230600	Genic enhancers	Spleen	Spleen
50	chr5:179228800-179230600	Enhancers	Monocytes-CD14+_RO01746	blood

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