Variant report

Variant	rs272440
Chromosome Location	chr5:179228623-179228624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179228149-179229233	MCF-7	breast:	n/a	n/a
2	POLR2A	chr5:179228182-179229253	GM12878	blood:	n/a	n/a
3	CTCF	chr5:179228405-179229422	A549	lung:	n/a	chr5:179229354-179229367 chr5:179229196-179229205
4	CTCF	chr5:179228500-179228650	GM12873	blood:	n/a	n/a
5	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
6	POLR2A	chr5:179227663-179229654	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr5:179228118-179229843	HL-60	blood:	n/a	n/a
8	POLR2A	chr5:179228463-179229544	A549	lung:	n/a	n/a
9	POLR2A	chr5:179228185-179228655	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:179227108-179228738	K562	blood:	n/a	n/a
11	POLR2A	chr5:179228262-179228712	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:179228412-179228649	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:179228473-179231388	HepG2	liver:	n/a	n/a
14	CTCF	chr5:179228608-179228641	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:179228429-179228660	ProgFib	skin:	n/a	n/a
16	POLR2A	chr5:179228348-179228725	A549	lung:	n/a	n/a
17	POLR2A	chr5:179228258-179228691	GM12892	blood:	n/a	n/a
18	RAD21	chr5:179228617-179229298	HCT-116	colon:	n/a	n/a
19	POLR2A	chr5:179224688-179234670	K562	blood:	n/a	n/a
20	POLR2A	chr5:179228504-179228653	A549	lung:	n/a	n/a
21	POLR2A	chr5:179228477-179228713	K562	blood:	n/a	n/a
22	POLR2A	chr5:179228297-179229178	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179227703..179229883-chr5:179285735..179289127,3	K562	blood:
2	chr5:179125163..179127622-chr5:179228110..179231035,2	K562	blood:
3	chr5:179227831..179231343-chr5:179333679..179336075,3	MCF-7	breast:
4	chr5:179227703..179229883-chr5:179285735..179288229,2	K562	blood:
5	chr5:179159678..179161359-chr5:179228559..179231556,2	MCF-7	breast:
6	chr5:179049178..179050682-chr5:179227339..179229062,2	MCF-7	breast:

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10063824	0.83[AMR][1000 genomes]
rs10078686	1.00[MEX][hapmap]
rs13171831	0.83[AMR][1000 genomes]
rs1552436	0.83[AMR][1000 genomes]
rs17079679	1.00[MEX][hapmap]
rs2450483	0.83[AMR][1000 genomes]
rs2516294	0.83[AMR][1000 genomes]
rs269459	1.00[MEX][hapmap]
rs272431	0.83[AMR][1000 genomes]
rs28611085	0.83[AMR][1000 genomes]
rs4391132	0.83[AMR][1000 genomes]
rs4643906	0.83[AMR][1000 genomes]
rs545136	0.83[AMR][1000 genomes]
rs562457	0.83[AMR][1000 genomes]
rs6601068	0.83[AMR][1000 genomes]
rs6601074	0.83[AMR][1000 genomes]
rs6872715	0.83[AMR][1000 genomes]
rs7717213	1.00[MEX][hapmap]
rs9329087	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv600661	chr5:179220010-179228623	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv600664	chr5:179221789-179228623	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	149 gene(s)	inside rSNPs	diseases
22	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
23	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
24	nsv600667	chr5:179223023-179229039	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	148 gene(s)	inside rSNPs	diseases
25	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
26	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	chr5:179223600-179228800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:179223800-179228800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:179223800-179229600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:179223800-179231600	Weak transcription	Fetal Kidney	kidney
5	chr5:179223800-179231600	Weak transcription	Psoas Muscle	Psoas
6	chr5:179224000-179228800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:179224000-179229000	Strong transcription	A549	lung
8	chr5:179224000-179229000	Strong transcription	NHLF	lung
9	chr5:179224000-179229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:179224000-179229200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:179224000-179229200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:179224000-179229400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:179224000-179229600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:179224000-179230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:179224000-179230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:179224000-179230000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:179224000-179230800	Weak transcription	Right Atrium	heart
18	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:179224200-179228800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:179224200-179228800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:179224200-179228800	Strong transcription	Fetal Intestine Small	intestine
22	chr5:179224200-179228800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr5:179224200-179229000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:179224200-179229000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:179224200-179229000	Weak transcription	GM12878-XiMat	blood
26	chr5:179224200-179229600	Weak transcription	NH-A	brain
27	chr5:179224200-179230000	Strong transcription	Brain Germinal Matrix	brain
28	chr5:179224400-179228800	Strong transcription	Fetal Muscle Leg	muscle
29	chr5:179224400-179228800	Strong transcription	Left Ventricle	heart
30	chr5:179224400-179228800	Strong transcription	Lung	lung
31	chr5:179224400-179229000	Strong transcription	Gastric	stomach
32	chr5:179224400-179229000	Weak transcription	Hela-S3	cervix
33	chr5:179224400-179229200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:179224400-179229200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:179224400-179229200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr5:179224400-179229600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:179224600-179228800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:179224600-179228800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:179225000-179228800	Strong transcription	Colonic Mucosa	Colon
40	chr5:179225400-179229200	Strong transcription	Fetal Intestine Large	intestine
41	chr5:179226200-179232200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:179226800-179233200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:179227000-179228800	Strong transcription	Fetal Stomach	stomach
44	chr5:179227000-179228800	Strong transcription	Spleen	Spleen
45	chr5:179227000-179229400	Weak transcription	Primary B cells from cord blood	blood
46	chr5:179227000-179230800	Weak transcription	Fetal Brain Male	brain
47	chr5:179227200-179228800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:179227200-179228800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:179227200-179229000	Weak transcription	Stomach Mucosa	stomach
50	chr5:179227200-179230200	Weak transcription	HUVEC	blood vessel

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