Variant report

Variant	rs566712228
Chromosome Location	chr5:60626569-60626570
allele	A/C
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	REST	chr5:60625830-60631210	H1-neurons	neurons:	n/a	chr5:60629395-60629408 chr5:60626655-60626668
2	PAX5	chr5:60626517-60627060	GM12892	blood:	n/a	chr5:60627009-60627018
3	POLR2A	chr5:60626174-60628500	HUVEC	blood vessel:	n/a	n/a
4	GATA3	chr5:60626267-60626644	T-47D	breast:	n/a	n/a
5	TCF7L2	chr5:60626088-60628038	Hela-S3	cervix:	n/a	chr5:60627651-60627660 chr5:60627648-60627662
6	HA-E2F1	chr5:60626203-60627569	MCF-7	breast:	n/a	chr5:60626897-60626911 chr5:60626705-60626715 chr5:60627410-60627419
7	MYC	chr5:60626553-60626638	MCF-7	breast:	n/a	n/a
8	TCF7L2	chr5:60626209-60626621	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr5:60626491-60627046	GM12892	blood:	n/a	n/a
10	TFAP2A	chr5:60626263-60627697	Hela-S3	cervix:	n/a	chr5:60627504-60627516 chr5:60626884-60626896 chr5:60627076-60627084 chr5:60626699-60626711 chr5:60627075-60627087 chr5:60626699-60626711
11	HA-E2F1	chr5:60626524-60628476	Hela-S3	cervix:	n/a	chr5:60626897-60626911 chr5:60627896-60627905 chr5:60627828-60627837 chr5:60626705-60626715 chr5:60627410-60627419
12	TCF12	chr5:60626122-60628395	ECC-1	luminal epithelium:	n/a	chr5:60627382-60627392
13	SRF	chr5:60626025-60628448	HCT-116	colon:	n/a	chr5:60627972-60627986 chr5:60627990-60628005 chr5:60627970-60627988 chr5:60627972-60627990 chr5:60627974-60627987 chr5:60627971-60627989 chr5:60627550-60627560 chr5:60627975-60627992 chr5:60627985-60627995 chr5:60627972-60627989
14	MAX	chr5:60626103-60628180	SK-N-SH	brain:	n/a	chr5:60627550-60627560 chr5:60627234-60627243 chr5:60627832-60627842
15	NFIC	chr5:60626214-60628196	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr5:60626434-60628244	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr5:60625558-60630285	Hela-S3	cervix:	n/a	n/a
18	CHD2	chr5:60626205-60628374	Hela-S3	cervix:	n/a	chr5:60627826-60627836
19	MAFK	chr5:60625724-60627683	Hela-S3	cervix:	n/a	chr5:60626128-60626143
20	GATA2	chr5:60626135-60627649	SH-SY5Y	brain:	n/a	n/a
21	RAD21	chr5:60626306-60627075	A549	lung:	n/a	n/a
22	POLR2A	chr5:60626147-60626665	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr5:60625341-60628382	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr5:60626057-60626735	SK-N-MC	brain:	n/a	n/a
25	ELK4	chr5:60626138-60626570	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr5:60626320-60627640	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:60626251-60626607	U87	brain:	n/a	n/a
28	TAF1	chr5:60626404-60627038	Hela-S3	cervix:	n/a	n/a
29	GATA2	chr5:60625552-60626658	HUVEC	blood vessel:	n/a	n/a
30	FOXM1	chr5:60626040-60626808	ECC-1	luminal epithelium:	n/a	n/a
31	YY1	chr5:60626396-60627126	HepG2	liver:	n/a	chr5:60626702-60626716 chr5:60627013-60627022 chr5:60627011-60627022 chr5:60626707-60626716
32	BACH1	chr5:60626449-60628467	H1-hESC	embryonic stem cell:	n/a	n/a
33	RUNX3	chr5:60626317-60626749	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:60625918-60628469	HUVEC	blood vessel:	n/a	n/a
35	TFAP2C	chr5:60626127-60627712	Hela-S3	cervix:	n/a	chr5:60627488-60627503
36	MXI1	chr5:60625150-60628551	IMR90	lung:	n/a	n/a
37	YY1	chr5:60626363-60627048	ECC-1	luminal epithelium:	n/a	chr5:60626369-60626380 chr5:60626702-60626716 chr5:60627013-60627022 chr5:60627011-60627022 chr5:60626707-60626716
38	MAZ	chr5:60626233-60628172	GM12878	blood:	n/a	chr5:60627550-60627560 chr5:60627234-60627243 chr5:60627832-60627842
39	CTCF	chr5:60626420-60626570	BJ	skin:	n/a	n/a
40	TEAD4	chr5:60626429-60628270	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr5:60626325-60626594	NB4	blood:	n/a	n/a
42	POLR2A	chr5:60626250-60628305	HEK293	kidney:	n/a	n/a
43	MAX	chr5:60626388-60628312	HepG2	liver:	n/a	chr5:60627550-60627560 chr5:60627234-60627243 chr5:60627832-60627842
44	RAD21	chr5:60626241-60627753	A549	lung:	n/a	chr5:60627693-60627703 chr5:60627693-60627705
45	RCOR1	chr5:60626314-60626620	K562	blood:	n/a	n/a
46	GATA3	chr5:60626129-60627181	MCF-7	breast:	n/a	n/a
47	POLR2A	chr5:60626363-60629610	MCF-7	breast:	n/a	n/a
48	RCOR1	chr5:60623071-60628252	IMR90	lung:	n/a	n/a
49	CHD1	chr5:60623202-60631624	IMR90	lung:	n/a	chr5:60629730-60629740 chr5:60629024-60629034 chr5:60629683-60629693 chr5:60629116-60629123 chr5:60629352-60629362 chr5:60627826-60627836
50	POLR2A	chr5:60626228-60628205	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
2	chr5:60463053..60463874-chr5:60626475..60627223,2	MCF-7	breast:
3	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
4	chr5:60626139..60628076-chr5:60895124..60897725,2	MCF-7	breast:
5	chr5:59993591..59996148-chr5:60625919..60628980,4	K562	blood:
6	chr5:60469553..60471380-chr5:60625380..60627759,2	MCF-7	breast:
7	chr12:53845725..53846383-chr5:60625600..60626600,2	Hela-S3	cervix:
8	chr5:60546830..60548400-chr5:60625408..60627597,2	MCF-7	breast:
9	chr5:60353410..60356120-chr5:60624338..60627119,3	MCF-7	breast:
10	chr5:60463125..60463841-chr5:60626532..60627147,2	MCF-7	breast:
11	chr5:60554941..60557365-chr5:60625053..60627690,3	MCF-7	breast:
12	chr5:60626093..60627678-chr5:60926976..60929648,2	MCF-7	breast:
13	chr5:60605123..60607843-chr5:60623875..60626572,3	MCF-7	breast:

Variant related genes	Relation type
ZSWIM6	TF binding region
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv19714	chr5:60625377-60629756	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv3471610	chr5:60625845-60630243	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv3471611	chr5:60625845-60630243	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv3502265	chr5:60626270-60630343	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv3502266	chr5:60626270-60630343	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1815974	chr5:60626344-60664356	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60624400-60626600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr5:60625000-60626800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr5:60625200-60626600	Flanking Active TSS	HUVEC	blood vessel
4	chr5:60625200-60630800	Active TSS	Colonic Mucosa	Colon
5	chr5:60625400-60631000	Active TSS	Brain Hippocampus Middle	brain
6	chr5:60625600-60626600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr5:60625600-60626600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr5:60625600-60626800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:60625600-60630600	Active TSS	Colon Smooth Muscle	Colon
10	chr5:60625600-60630800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:60625600-60630800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:60625600-60631000	Active TSS	Brain Anterior Caudate	brain
13	chr5:60625800-60626600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:60625800-60626600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:60625800-60626600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:60625800-60626600	Active TSS	Fetal Brain Male	brain
17	chr5:60625800-60626600	Active TSS	Stomach Smooth Muscle	stomach
18	chr5:60625800-60627400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr5:60625800-60628800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:60625800-60628800	Active TSS	Brain Germinal Matrix	brain
21	chr5:60625800-60630000	Active TSS	Fetal Lung	lung
22	chr5:60625800-60630200	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr5:60625800-60630400	Active TSS	Fetal Brain Female	brain
24	chr5:60625800-60630800	Active TSS	NHDF-Ad	bronchial
25	chr5:60625800-60631000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr5:60625800-60631000	Active TSS	HSMM	muscle
27	chr5:60626000-60626600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr5:60626000-60626600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr5:60626000-60626600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr5:60626000-60626600	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr5:60626000-60626600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr5:60626000-60626600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:60626000-60626600	Flanking Active TSS	HMEC	breast
34	chr5:60626000-60626600	Flanking Active TSS	NHEK	skin
35	chr5:60626000-60626800	Flanking Active TSS	Placenta	Placenta
36	chr5:60626000-60627000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:60626000-60627200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr5:60626000-60627200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr5:60626000-60627400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr5:60626000-60627800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:60626000-60627800	Active TSS	Fetal Heart	heart
42	chr5:60626000-60628200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:60626000-60629400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:60626000-60629600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:60626000-60629800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:60626000-60629800	Active TSS	Primary T cells from cord blood	blood
47	chr5:60626000-60630000	Active TSS	Psoas Muscle	Psoas
48	chr5:60626000-60630000	Active TSS	Rectal Smooth Muscle	rectum
49	chr5:60626000-60630000	Active TSS	Hela-S3	cervix
50	chr5:60626000-60630200	Active TSS	Pancreas	Pancrea

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