Variant report

Variant	rs550816740
Chromosome Location	chr5:60625606-60625607
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	FOSL2	chr5:60625558-60625968	HepG2	liver:	n/a	chr5:60625806-60625817
2	POLR2A	chr5:60625566-60625978	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr5:60625382-60626284	HUVEC	blood vessel:	n/a	chr5:60625807-60625818
4	POLR2A	chr5:60625558-60630285	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:60625341-60628382	HUVEC	blood vessel:	n/a	n/a
6	GATA2	chr5:60625552-60626658	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr5:60625150-60628551	IMR90	lung:	n/a	n/a
8	RCOR1	chr5:60623071-60628252	IMR90	lung:	n/a	n/a
9	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
10	KAP1	chr5:60624848-60626830	HEK293	kidney:	n/a	n/a
11	RAD21	chr5:60625559-60627319	Hela-S3	cervix:	n/a	n/a
12	ZKSCAN1	chr5:60625470-60625982	Hela-S3	cervix:	n/a	n/a
13	KAP1	chr5:60625602-60626704	U2OS	brain:	n/a	n/a
14	STAT1	chr5:60625199-60625826	Hela-S3	cervix:	n/a	chr5:60625526-60625540 chr5:60625523-60625543 chr5:60625527-60625538 chr5:60625528-60625537 chr5:60625529-60625538 chr5:60625529-60625537 chr5:60625523-60625543
15	POLR2A	chr5:60625447-60627903	HUVEC	blood vessel:	n/a	n/a
16	MXI1	chr5:60625218-60631493	SK-N-SH	brain:	n/a	n/a
17	SMC3	chr5:60625505-60627719	Hela-S3	cervix:	n/a	chr5:60627693-60627703 chr5:60626856-60626870 chr5:60625619-60625626 chr5:60626837-60626847 chr5:60626859-60626869
18	NFIC	chr5:60625604-60626077	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:60623868-60631522	IMR90	lung:	n/a	n/a
20	HCFC1	chr5:60625212-60628404	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr5:60625325-60627722	IMR90	lung:	n/a	chr5:60627693-60627703 chr5:60627693-60627705
22	POLR2A	chr5:60625240-60628184	HUVEC	blood vessel:	n/a	n/a
23	MTA3	chr5:60625566-60626056	GM12878	blood:	n/a	n/a
24	PAX5	chr5:60625602-60625973	GM12891	blood:	n/a	n/a
25	MAZ	chr5:60623153-60628543	IMR90	lung:	n/a	chr5:60627550-60627560 chr5:60623720-60623729 chr5:60627234-60627243 chr5:60627832-60627842 chr5:60623721-60623730

No.	Distal block	Cell Line	Cell type
1	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
2	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
3	chr5:60469553..60471380-chr5:60625380..60627759,2	MCF-7	breast:
4	chr12:53845725..53846383-chr5:60625600..60626600,2	Hela-S3	cervix:
5	chr5:60546830..60548400-chr5:60625408..60627597,2	MCF-7	breast:
6	chr5:60621987..60625726-chr5:60627235..60630400,4	MCF-7	breast:
7	chr5:60353410..60356120-chr5:60624338..60627119,3	MCF-7	breast:
8	chr5:60623389..60626002-chr5:60627972..60629688,3	K562	blood:
9	chr5:60554941..60557365-chr5:60625053..60627690,3	MCF-7	breast:
10	chr5:60605123..60607843-chr5:60623875..60626572,3	MCF-7	breast:

Variant related genes	Relation type
ZSWIM6	TF binding region
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60616800-60625800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:60617000-60626200	Weak transcription	Esophagus	oesophagus
3	chr5:60619400-60626200	Weak transcription	Small Intestine	intestine
4	chr5:60623200-60625800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:60623200-60626000	Enhancers	HMEC	breast
6	chr5:60623400-60626000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:60623600-60625800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:60623600-60626000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:60623600-60626000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:60623600-60626000	Enhancers	NHEK	skin
11	chr5:60623600-60626200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:60623800-60625800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:60623800-60625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:60623800-60626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:60623800-60626400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr5:60624000-60626000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:60624200-60625800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:60624200-60625800	Enhancers	HSMMtube	muscle
19	chr5:60624200-60626000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:60624200-60626000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:60624400-60625800	Enhancers	Fetal Brain Male	brain
22	chr5:60624400-60626000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:60624400-60626000	Enhancers	Fetal Heart	heart
24	chr5:60624400-60626000	Enhancers	Placenta	Placenta
25	chr5:60624400-60626200	Bivalent Enhancer	GM12878-XiMat	blood
26	chr5:60624400-60626600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr5:60624600-60626000	Enhancers	Fetal Muscle Leg	muscle
28	chr5:60624600-60626000	Enhancers	Pancreas	Pancrea
29	chr5:60624600-60626000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr5:60624600-60626000	Enhancers	Stomach Mucosa	stomach
31	chr5:60624600-60626000	Flanking Active TSS	NHLF	lung
32	chr5:60624800-60625800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:60624800-60625800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:60624800-60625800	Enhancers	NHDF-Ad	bronchial
35	chr5:60624800-60626000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:60624800-60626200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr5:60624800-60626200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr5:60625000-60625800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr5:60625000-60625800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:60625000-60625800	Enhancers	Brain Germinal Matrix	brain
41	chr5:60625000-60625800	Flanking Active TSS	Fetal Lung	lung
42	chr5:60625000-60625800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr5:60625000-60626000	Enhancers	Primary B cells from peripheral blood	blood
44	chr5:60625000-60626000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:60625000-60626000	Weak transcription	Right Atrium	heart
46	chr5:60625000-60626800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr5:60625200-60625800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:60625200-60625800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr5:60625200-60625800	Flanking Active TSS	HSMM	muscle
50	chr5:60625200-60626000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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