Variant report

Variant	rs550597300
Chromosome Location	chr3:150478360-150478361
allele	G/T
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	chr3:150476883-150483109	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:150477871-150479157	K562	blood:	n/a	n/a
3	TBP	chr3:150478164-150478529	K562	blood:	n/a	n/a
4	TAF7	chr3:150478026-150478372	K562	blood:	n/a	n/a
5	EP300	chr3:150477983-150478453	K562	blood:	n/a	n/a
6	POLR2A	chr3:150478152-150478567	MCF10A-Er-Src	breast:	n/a	n/a
7	YY1	chr3:150478271-150478672	GM12878	blood:	n/a	n/a
8	SIN3A	chr3:150478288-150478709	GM12878	blood:	n/a	n/a
9	RELA	chr3:150477976-150478914	GM10847	blood:	n/a	n/a
10	BCL3	chr3:150478029-150478765	GM12878	blood:	n/a	chr3:150478323-150478332
11	IKZF1	chr3:150478069-150478673	GM12878	blood:	n/a	n/a
12	RELA	chr3:150477126-150479001	GM12891	blood:	n/a	n/a
13	MXI1	chr3:150478072-150478837	GM12878	blood:	n/a	n/a
14	PAX5	chr3:150478121-150478389	GM12878	blood:	n/a	chr3:150478323-150478332
15	POLR2A	chr3:150477494-150478364	HepG2	liver:	n/a	n/a
16	ATF2	chr3:150477935-150478865	GM12878	blood:	n/a	n/a
17	STAT5A	chr3:150478080-150478893	GM12878	blood:	n/a	chr3:150478231-150478239 chr3:150478228-150478242 chr3:150478323-150478334
18	RELA	chr3:150478064-150478812	GM19193	blood:	n/a	n/a
19	POU2F2	chr3:150478338-150478880	GM12878	blood:	n/a	chr3:150478665-150478674 chr3:150478658-150478680 chr3:150478666-150478673 chr3:150478663-150478674 chr3:150478665-150478675 chr3:150478665-150478673 chr3:150478664-150478674 chr3:150478662-150478676 chr3:150478665-150478675 chr3:150478660-150478678 chr3:150478556-150478568
20	RELA	chr3:150477803-150478875	GM18505	blood:	n/a	n/a
21	WRNIP1	chr3:150477002-150478876	GM12878	blood:	n/a	n/a
22	CHD2	chr3:150478141-150478742	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:150477831-150478389	GM12891	blood:	n/a	n/a
24	YY1	chr3:150478351-150478688	GM12891	blood:	n/a	n/a
25	CEBPB	chr3:150477921-150478902	GM12878	blood:	n/a	n/a
26	MTA3	chr3:150477787-150479126	GM12878	blood:	n/a	n/a
27	MEF2A	chr3:150478277-150478926	GM12878	blood:	n/a	chr3:150478894-150478910 chr3:150478894-150478909 chr3:150478804-150478819 chr3:150478805-150478816 chr3:150478804-150478818
28	MXI1	chr3:150477822-150483051	SK-N-SH	brain:	n/a	n/a
29	ARID3A	chr3:150478321-150478599	K562	blood:	n/a	n/a
30	NFIC	chr3:150477904-150479143	GM12878	blood:	n/a	n/a
31	IRF4	chr3:150478048-150478748	GM12878	blood:	n/a	chr3:150478321-150478335
32	POLR2A	chr3:150478019-150478391	GM12891	blood:	n/a	n/a
33	RELA	chr3:150477993-150478777	GM18951	blood:	n/a	n/a
34	POLR2A	chr3:150477882-150478366	GM12892	blood:	n/a	n/a
35	YY1	chr3:150478320-150478681	GM12892	blood:	n/a	n/a
36	TBP	chr3:150478028-150479324	GM12878	blood:	n/a	chr3:150478721-150478732
37	EBF1	chr3:150478190-150478603	GM12878	blood:	n/a	chr3:150478369-150478380
38	PAX5	chr3:150477991-150478565	GM12878	blood:	n/a	chr3:150478323-150478332
39	EP300	chr3:150478209-150478810	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:150478010-150478394	MCF10A-Er-Src	breast:	n/a	n/a
41	EP300	chr3:150478229-150478835	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:150478040-150478480	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:150477947-150478376	K562	blood:	n/a	n/a
44	MAZ	chr3:150478178-150478914	GM12878	blood:	n/a	n/a
45	MTA3	chr3:150478031-150479530	GM12878	blood:	n/a	n/a
46	PML	chr3:150477267-150478962	GM12878	blood:	n/a	n/a
47	IRF3	chr3:150478066-150478730	GM12878	blood:	n/a	chr3:150478320-150478334 chr3:150478323-150478334 chr3:150478321-150478334 chr3:150478321-150478335 chr3:150478322-150478339 chr3:150478328-150478335 chr3:150478321-150478334 chr3:150478323-150478333 chr3:150478319-150478333 chr3:150478323-150478337 chr3:150478321-150478334
48	NRF1	chr3:150478319-150478654	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:150477697-150478978	GM12878	blood:	n/a	n/a
50	RUNX3	chr3:150477907-150478821	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:150379555..150382214-chr3:150476705..150479002,2	K562	blood:
2	chr3:150319354..150323687-chr3:150477863..150484487,11	MCF-7	breast:
3	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
4	chr3:150476989..150478844-chr3:150495018..150496645,2	MCF-7	breast:
5	chr3:150125257..150128558-chr3:150478258..150482422,4	K562	blood:
6	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

Variant related genes	Relation type
SIAH2-AS1	TF binding region
ENSG00000144895	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000244668	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv592035	chr3:150478018-150481021	Flanking Active TSS Enhancers Weak transcription Active TSS 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	32 gene(s)	inside rSNPs	n/a
3	nsv592036	chr3:150478018-150481236	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	n/a
4	esv1820145	chr3:150478018-150487945	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150457000-150478800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:150463000-150478400	Weak transcription	HSMM	muscle
3	chr3:150470000-150478800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:150471200-150479600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:150471600-150479600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:150474000-150478800	Enhancers	Small Intestine	intestine
7	chr3:150475000-150479800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr3:150475400-150480400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:150477000-150478400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:150477000-150479000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:150477000-150479400	Flanking Active TSS	Liver	Liver
12	chr3:150477000-150479400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:150477200-150479800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr3:150477200-150480400	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr3:150477400-150478400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:150477400-150478600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:150477400-150478800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:150477400-150480000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:150477600-150478400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:150477600-150478600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:150477600-150478600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:150477600-150479000	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr3:150477600-150479200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:150477600-150479200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr3:150477600-150479200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr3:150477600-150479200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:150477600-150479600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:150477600-150479600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr3:150477600-150479800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:150477600-150480200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:150477600-150480400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:150477800-150478400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:150477800-150478400	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr3:150477800-150478400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:150477800-150478400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:150477800-150478400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:150477800-150478400	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr3:150477800-150478600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:150477800-150478800	Enhancers	Fetal Intestine Large	intestine
40	chr3:150477800-150478800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr3:150477800-150478800	Transcr. at gene 5' and 3'	K562	blood
42	chr3:150477800-150478800	Flanking Active TSS	NHLF	lung
43	chr3:150477800-150479000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:150477800-150479000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:150477800-150479000	Enhancers	Brain Substantia Nigra	brain
46	chr3:150477800-150479000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:150477800-150479400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:150477800-150479400	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr3:150477800-150479400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:150477800-150479400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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