Variant report

Variant	rs55744247
Chromosome Location	chr5:52777864-52777865
allele	A/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	ELK1	chr5:52777754-52777937	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr5:52777826-52777987	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr5:52777754-52778114	GM12878	blood:	n/a	chr5:52777853-52777862
4	POLR2A	chr5:52777611-52778241	MCF10A-Er-Src	breast:	n/a	n/a
5	EGR1	chr5:52777711-52777984	K562	blood:	n/a	chr5:52777964-52777974 chr5:52777856-52777866 chr5:52777900-52777910 chr5:52777851-52777864
6	CHD1	chr5:52773963-52779659	IMR90	lung:	n/a	chr5:52776596-52776606 chr5:52777700-52777710 chr5:52776601-52776611
7	POLR2A	chr5:52777756-52777939	A549	lung:	n/a	n/a
8	MAZ	chr5:52777719-52778041	HepG2	liver:	n/a	chr5:52777853-52777862
9	CEBPB	chr5:52777674-52778018	HepG2	liver:	n/a	chr5:52777928-52777939
10	CTCF	chr5:52777820-52777970	HPF	lung:	n/a	n/a
11	SIN3A	chr5:52777671-52779208	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:52777561-52778038	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr5:52777764-52778126	IMR90	lung:	n/a	n/a
14	RAD21	chr5:52776262-52779138	IMR90	lung:	n/a	chr5:52776513-52776525 chr5:52776611-52776621
15	POLR2A	chr5:52775052-52780368	SK-N-SH	brain:	n/a	n/a
16	CHD2	chr5:52777238-52778083	Hela-S3	cervix:	n/a	chr5:52777700-52777710
17	RAD21	chr5:52777805-52778044	K562	blood:	n/a	n/a
18	CTCF	chr5:52777860-52778010	GM12864	blood:	n/a	n/a
19	POLR2A	chr5:52777446-52778224	U87	brain:	n/a	n/a
20	RAD21	chr5:52777643-52778079	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr5:52777710-52777987	K562	blood:	n/a	n/a
22	CEBPB	chr5:52777560-52778264	MCF-7	breast:	n/a	chr5:52777928-52777939
23	PRDM1	chr5:52777369-52777896	Hela-S3	cervix:	n/a	chr5:52777723-52777736 chr5:52777723-52777732 chr5:52777721-52777736
24	TFAP2A	chr5:52777721-52778107	Hela-S3	cervix:	n/a	chr5:52777835-52777850
25	TAF1	chr5:52777628-52777932	SK-N-SH	brain:	n/a	n/a
26	EP300	chr5:52777619-52778016	Hela-S3	cervix:	n/a	chr5:52777849-52777865
27	MAX	chr5:52777624-52778070	ECC-1	luminal epithelium:	n/a	chr5:52777853-52777862
28	MXI1	chr5:52775095-52779435	IMR90	lung:	n/a	n/a
29	FOXP2	chr5:52777772-52778010	PFSK-1	brain:	n/a	n/a
30	CEBPB	chr5:52777707-52778124	HepG2	liver:	n/a	chr5:52777928-52777939
31	ZBTB7A	chr5:52777824-52777985	K562	blood:	n/a	n/a
32	TAF1	chr5:52777600-52778071	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr5:52777626-52778075	U87	brain:	n/a	n/a
34	CEBPB	chr5:52777703-52778078	K562	blood:	n/a	chr5:52777928-52777939
35	EGR1	chr5:52777710-52777984	K562	blood:	n/a	chr5:52777964-52777974 chr5:52777856-52777866 chr5:52777900-52777910 chr5:52777851-52777864
36	POLR2A	chr5:52777674-52778149	HL-60	blood:	n/a	n/a
37	CEBPB	chr5:52777727-52778103	H1-hESC	embryonic stem cell:	n/a	chr5:52777928-52777939
38	STAT3	chr5:52777813-52777978	MCF10A-Er-Src	breast:	n/a	n/a
39	IRF1	chr5:52777841-52778083	K562	blood:	n/a	chr5:52778009-52778021 chr5:52778006-52778020 chr5:52778004-52778021 chr5:52778010-52778024 chr5:52778010-52778020 chr5:52778009-52778021 chr5:52778004-52778018 chr5:52778009-52778020 chr5:52778002-52778022 chr5:52778008-52778019
40	E2F6	chr5:52777539-52778183	A549	lung:	n/a	n/a
41	MXI1	chr5:52777781-52777981	H1-hESC	embryonic stem cell:	n/a	n/a
42	TFAP2C	chr5:52777661-52778144	Hela-S3	cervix:	n/a	n/a
43	HDAC2	chr5:52777750-52778070	HepG2	liver:	n/a	chr5:52778003-52778017
44	HA-E2F1	chr5:52777544-52778508	MCF-7	breast:	n/a	n/a
45	UBTF	chr5:52777558-52778139	K562	blood:	n/a	n/a
46	CTCF	chr5:52777780-52777930	GM12872	blood:	n/a	n/a
47	POLR2A	chr5:52777694-52778107	HL-60	blood:	n/a	n/a
48	BHLHE40	chr5:52777779-52778035	K562	blood:	n/a	n/a
49	CTCF	chr5:52777860-52778010	AG04449	skin:	n/a	n/a
50	CHD2	chr5:52777808-52778003	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52777363..52778020-chr5:53513424..53514366,2	MCF-7	breast:

Variant related genes	Relation type
FST	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11951646	0.82[ASN][1000 genomes]
rs11957312	0.82[ASN][1000 genomes]
rs11958349	0.82[ASN][1000 genomes]
rs3943928	0.82[ASN][1000 genomes]
rs55662636	0.82[ASN][1000 genomes]
rs55873647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62359324	0.82[ASN][1000 genomes]
rs62359325	0.82[ASN][1000 genomes]
rs62370471	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370472	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370473	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370474	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62370480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748110	0.82[ASN][1000 genomes]
rs72748111	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52774200-52778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:52774200-52778800	Active TSS	Osteobl	bone
4	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
5	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:52774400-52778200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:52774400-52778400	Active TSS	Right Ventricle	heart
8	chr5:52774400-52778400	Bivalent/Poised TSS	Thymus	Thymus
9	chr5:52774400-52778600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:52774400-52778600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr5:52774400-52778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52774400-52778600	Active TSS	Aorta	Aorta
13	chr5:52774400-52778800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:52774400-52778800	Active TSS	Hela-S3	cervix
15	chr5:52774400-52778800	Active TSS	HSMM	muscle
16	chr5:52774400-52778800	Active TSS	HSMMtube	muscle
17	chr5:52774400-52778800	Active TSS	NHDF-Ad	bronchial
18	chr5:52774400-52779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr5:52774400-52779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:52774400-52779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:52774400-52779000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:52774400-52779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:52774400-52779000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:52774400-52779000	Active TSS	Gastric	stomach
25	chr5:52774400-52779000	Active TSS	Psoas Muscle	Psoas
26	chr5:52774400-52779000	Active TSS	A549	lung
27	chr5:52774400-52779200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:52774400-52779200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:52774400-52779200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:52774400-52779400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:52774600-52778200	Active TSS	NHEK	skin
32	chr5:52774600-52778600	Active TSS	NHLF	lung
33	chr5:52774600-52778800	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr5:52774600-52779200	Active TSS	Rectal Smooth Muscle	rectum
35	chr5:52774800-52778400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
36	chr5:52774800-52778600	Active TSS	HMEC	breast
37	chr5:52775000-52778800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:52775200-52778800	Bivalent/Poised TSS	HepG2	liver
39	chr5:52775200-52779000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:52775400-52778000	Active TSS	Lung	lung
41	chr5:52776000-52778200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:52776400-52778000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:52776600-52778000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:52776600-52779400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr5:52776800-52778000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:52776800-52778400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:52776800-52778400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
48	chr5:52776800-52778600	Active TSS	Right Atrium	heart
49	chr5:52777000-52778400	Active TSS	NH-A	brain
50	chr5:52777000-52778600	Active TSS	Left Ventricle	heart

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