Variant report

Variant	rs27646
Chromosome Location	chr5:52285077-52285078
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	chr5:52284680-52285568	A549	lung:	n/a	n/a
2	FOXA1	chr5:52284883-52285202	T-47D	breast:	n/a	n/a
3	MAZ	chr5:52284888-52285417	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:52284781-52285391	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:52284721-52285802	A549	lung:	n/a	n/a
6	CTCF	chr5:52285060-52285210	HCPEpiC	choroid plexus:	n/a	n/a
7	POLR2A	chr5:52284987-52285593	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr5:52284560-52285626	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr5:52284623-52285962	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr5:52284653-52285634	A549	lung:	n/a	chr5:52285000-52285007
11	NFIC	chr5:52284634-52285312	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:52284849-52285337	SK-N-SH	brain:	n/a	n/a
13	EGR1	chr5:52284523-52285498	HCT-116	colon:	n/a	chr5:52284854-52284867 chr5:52284856-52284866 chr5:52284856-52284866 chr5:52284853-52284868 chr5:52284855-52284866 chr5:52284857-52284866 chr5:52284857-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284868
14	E2F4	chr5:52285024-52286136	MCF10A-Er-Src	breast:	n/a	chr5:52285766-52285776
15	ZKSCAN1	chr5:52284889-52286077	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:52284680-52285415	A549	lung:	n/a	n/a
17	MAX	chr5:52284578-52286032	MCF-7	breast:	n/a	n/a
18	POLR2A	chr5:52284380-52286686	HepG2	liver:	n/a	n/a
19	POLR2A	chr5:52284718-52285382	U87	brain:	n/a	n/a
20	MAZ	chr5:52284909-52285236	K562	blood:	n/a	n/a
21	POLR2A	chr5:52284650-52285395	HCT-116	colon:	n/a	n/a
22	POLR2A	chr5:52284776-52285721	MCF-7	breast:	n/a	n/a
23	REST	chr5:52284821-52285490	HepG2	liver:	n/a	n/a
24	FOSL2	chr5:52284792-52285435	HepG2	liver:	n/a	n/a
25	RFX5	chr5:52284950-52286303	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:52284651-52285937	MCF-7	breast:	n/a	n/a
27	POLR2A	chr5:52284778-52286247	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr5:52284813-52286212	Hela-S3	cervix:	n/a	n/a
29	RAD21	chr5:52284909-52285335	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:52284504-52286792	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr5:52284885-52285955	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr5:52284731-52285575	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:52284919-52285365	ProgFib	skin:	n/a	n/a
34	SIN3A	chr5:52284732-52286051	H1-hESC	embryonic stem cell:	n/a	chr5:52284833-52284847 chr5:52284780-52284789 chr5:52285687-52285697
35	MAX	chr5:52284418-52286296	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr5:52284446-52285269	T-47D	breast:	n/a	n/a
37	SP1	chr5:52284361-52285479	A549	lung:	n/a	chr5:52284859-52284868 chr5:52284858-52284870 chr5:52284858-52284870 chr5:52284859-52284869
38	POLR2A	chr5:52283218-52289712	MCF10A-Er-Src	breast:	n/a	n/a
39	ZBTB7A	chr5:52284941-52285088	HepG2	liver:	n/a	n/a
40	POLR2A	chr5:52284817-52285199	ECC-1	luminal epithelium:	n/a	n/a
41	TAF1	chr5:52284857-52286028	A549	lung:	n/a	n/a
42	EGR1	chr5:52284578-52285149	ECC-1	luminal epithelium:	n/a	chr5:52284854-52284867 chr5:52284856-52284866 chr5:52284856-52284866 chr5:52284853-52284868 chr5:52284855-52284866 chr5:52284857-52284866 chr5:52284857-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284867 chr5:52284854-52284868
43	POLR2A	chr5:52284777-52285460	HepG2	liver:	n/a	n/a
44	TBP	chr5:52285030-52285551	Hela-S3	cervix:	n/a	n/a
45	MAX	chr5:52284380-52286140	A549	lung:	n/a	n/a
46	MAX	chr5:52284794-52286004	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAZ	chr5:52284585-52286254	Hela-S3	cervix:	n/a	n/a
48	CEBPB	chr5:52284934-52285143	HepG2	liver:	n/a	n/a
49	MXI1	chr5:52284572-52286731	IMR90	lung:	n/a	n/a
50	MAX	chr5:52284808-52286035	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:41465200..41466185-chr5:52284727..52285281,2	Hela-S3	cervix:
2	chr1:110090680..110091547-chr5:52284624..52285607,2	Hela-S3	cervix:
3	chr3:169491018..169491750-chr5:52284853..52285673,2	Hela-S3	cervix:
4	chr5:52284713..52285560-chr7:107383991..107384708,2	Hela-S3	cervix:
5	chr1:155903642..155904437-chr5:52284658..52285227,2	Hela-S3	cervix:
6	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
7	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:

Variant related genes	Relation type
ITGA2	TF binding region
ENSG00000247796	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000241764	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000105879	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000065135	Chromatin interaction
ENSG00000272123	Chromatin interaction
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1904166	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27504	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27915	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28051	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35233	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35234	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6450097	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52284000-52288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:52284200-52285400	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr5:52284200-52286400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:52284200-52286600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:52284400-52285200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
6	chr5:52284400-52285200	Active TSS	Brain Angular Gyrus	brain
7	chr5:52284400-52285200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:52284400-52285200	Active TSS	Fetal Intestine Large	intestine
9	chr5:52284400-52285200	Enhancers	Placenta	Placenta
10	chr5:52284400-52285400	Active TSS	Rectal Smooth Muscle	rectum
11	chr5:52284400-52285600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:52284400-52285800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr5:52284400-52286200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:52284400-52286200	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr5:52284400-52286400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr5:52284400-52286400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:52284400-52286400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr5:52284400-52286600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr5:52284400-52286600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr5:52284400-52286600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:52284400-52286600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:52284400-52286800	Active TSS	Brain Substantia Nigra	brain
23	chr5:52284400-52287000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr5:52284600-52285200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:52284600-52285200	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
26	chr5:52284600-52285200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
27	chr5:52284600-52285400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:52284600-52285400	Active TSS	Brain Anterior Caudate	brain
29	chr5:52284600-52285400	Active TSS	Left Ventricle	heart
30	chr5:52284600-52285400	Active TSS	Right Atrium	heart
31	chr5:52284600-52285400	Active TSS	Spleen	Spleen
32	chr5:52284600-52285400	Active TSS	HSMM	muscle
33	chr5:52284600-52285600	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr5:52284600-52285800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:52284600-52285800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:52284600-52285800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr5:52284600-52285800	Active TSS	Colon Smooth Muscle	Colon
38	chr5:52284600-52285800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
39	chr5:52284600-52285800	Active TSS	Psoas Muscle	Psoas
40	chr5:52284600-52286000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:52284600-52286000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr5:52284600-52286000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
43	chr5:52284600-52286000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:52284600-52286200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:52284600-52286200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:52284600-52286200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr5:52284600-52286200	Active TSS	Gastric	stomach
48	chr5:52284600-52286200	Active TSS	Ovary	ovary
49	chr5:52284600-52286200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr5:52284600-52286400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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