Variant report

Variant	rs562457
Chromosome Location	chr5:179225768-179225769
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	POLR2A	chr5:179225482-179226924	K562	blood:	n/a	n/a
2	POLR2A	chr5:179225584-179226486	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
4	POLR2A	chr5:179225662-179226024	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:179225665-179227029	HL-60	blood:	n/a	n/a
6	POLR2A	chr5:179225579-179225832	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:179224688-179234670	K562	blood:	n/a	n/a
8	POLR2A	chr5:179225459-179226638	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179049042..179051273-chr5:179225764..179228331,2	MCF-7	breast:
2	chr5:179221892..179226661-chr5:179285311..179287197,6	MCF-7	breast:

Variant related genes	Relation type
MIR1229	TF binding region
ENSG00000161010	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10063824	1.00[AMR][1000 genomes]
rs13171831	1.00[AMR][1000 genomes]
rs1552436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2450483	1.00[AMR][1000 genomes]
rs2516294	1.00[AMR][1000 genomes]
rs272431	1.00[AMR][1000 genomes]
rs272440	0.83[AMR][1000 genomes]
rs28611085	1.00[AMR][1000 genomes]
rs4391132	1.00[AMR][1000 genomes]
rs4643906	1.00[AMR][1000 genomes]
rs4700837	0.83[AMR][1000 genomes]
rs545136	1.00[AMR][1000 genomes]
rs6601068	1.00[AMR][1000 genomes]
rs6601074	1.00[AMR][1000 genomes]
rs6872508	0.83[AMR][1000 genomes]
rs6872715	1.00[AMR][1000 genomes]
rs9329087	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv600663	chr5:179221789-179228369	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	148 gene(s)	inside rSNPs	diseases
23	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
24	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
25	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
26	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
27	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

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	chr5:179224000-179226000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:179224000-179226000	Weak transcription	NHDF-Ad	bronchial
8	chr5:179224000-179227400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:179224000-179227400	Strong transcription	Thymus	Thymus
10	chr5:179224000-179228200	Strong transcription	Fetal Thymus	thymus
11	chr5:179224000-179228400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr5:179224000-179228400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:179224000-179228600	Strong transcription	Dnd41	blood
14	chr5:179224000-179228800	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:179224000-179229000	Strong transcription	A549	lung
16	chr5:179224000-179229000	Strong transcription	NHLF	lung
17	chr5:179224000-179229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:179224000-179229200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:179224000-179229200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:179224000-179229400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:179224000-179229600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:179224000-179230000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:179224000-179230000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:179224000-179230000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:179224000-179230800	Weak transcription	Right Atrium	heart
26	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:179224200-179225800	Weak transcription	HSMM	muscle
28	chr5:179224200-179226200	Weak transcription	Fetal Brain Male	brain
29	chr5:179224200-179227400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179224200-179227800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:179224200-179227800	Weak transcription	Fetal Heart	heart
32	chr5:179224200-179228000	Strong transcription	Brain Anterior Caudate	brain
33	chr5:179224200-179228200	Strong transcription	Colon Smooth Muscle	Colon
34	chr5:179224200-179228400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:179224200-179228400	Strong transcription	Brain Hippocampus Middle	brain
36	chr5:179224200-179228400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:179224200-179228400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr5:179224200-179228600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:179224200-179228600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179224200-179228600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr5:179224200-179228600	Strong transcription	Fetal Brain Female	brain
42	chr5:179224200-179228800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:179224200-179228800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:179224200-179228800	Strong transcription	Fetal Intestine Small	intestine
45	chr5:179224200-179228800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr5:179224200-179229000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:179224200-179229000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr5:179224200-179229000	Weak transcription	GM12878-XiMat	blood
49	chr5:179224200-179229600	Weak transcription	NH-A	brain
50	chr5:179224200-179230000	Strong transcription	Brain Germinal Matrix	brain

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