Variant report

Variant	rs545169537
Chromosome Location	chr3:160822799-160822800
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	POLR2A	chr3:160822503-160823353	ProgFib	skin:	n/a	n/a
2	GABPA	chr3:160822071-160823714	MCF-7	breast:	n/a	n/a
3	MAX	chr3:160822234-160823527	HCT-116	colon:	n/a	n/a
4	TBP	chr3:160822375-160823386	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:160822778-160823192	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr3:160822700-160823318	GM12891	blood:	n/a	chr3:160822736-160822750 chr3:160822723-160822737 chr3:160822718-160822732
7	TEAD4	chr3:160822190-160823454	H1-hESC	embryonic stem cell:	n/a	chr3:160822474-160822483
8	ELF1	chr3:160822220-160823507	MCF-7	breast:	n/a	chr3:160823439-160823450
9	MAX	chr3:160822276-160823468	MCF-7	breast:	n/a	n/a
10	STAT3	chr3:160822796-160822977	MCF10A-Er-Src	breast:	n/a	chr3:160822928-160822939
11	CTCF	chr3:160822700-160822850	GM12866	blood:	n/a	n/a
12	CTCF	chr3:160822760-160822910	Caco-2	colon:	n/a	n/a
13	POLR2A	chr3:160822377-160823203	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr3:160822320-160823501	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:160822192-160823442	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:160822440-160823333	Gliobla	brain:	n/a	n/a
17	POLR2A	chr3:160822640-160823286	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:160822522-160823338	GM18951	blood:	n/a	n/a
19	MAX	chr3:160821640-160823909	MCF-7	breast:	n/a	n/a
20	RAD21	chr3:160822293-160822839	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:160822522-160823377	GM19099	blood:	n/a	n/a
22	HA-E2F1	chr3:160822200-160823635	MCF-7	breast:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
23	POLR2A	chr3:160822548-160823301	GM15510	blood:	n/a	n/a
24	MAX	chr3:160822746-160823369	K562	blood:	n/a	n/a
25	PML	chr3:160822413-160823258	MCF-7	breast:	n/a	n/a
26	STAT3	chr3:160822796-160823076	MCF10A-Er-Src	breast:	n/a	chr3:160822928-160822939
27	BACH1	chr3:160822337-160823250	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr3:160822490-160823333	MCF-7	breast:	n/a	n/a
29	POLR2A	chr3:160822628-160822843	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr3:160822386-160823399	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:160822362-160822827	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:160822529-160823345	HUVEC	blood vessel:	n/a	n/a
33	E2F6	chr3:160822061-160823742	H1-hESC	embryonic stem cell:	n/a	chr3:160823207-160823221 chr3:160823210-160823224 chr3:160822776-160822788
34	JUND	chr3:160822284-160822834	H1-hESC	embryonic stem cell:	n/a	n/a
35	HDAC2	chr3:160821953-160823716	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:160822720-160822870	AG04449	skin:	n/a	n/a
37	POLR2A	chr3:160822639-160823140	HCT-116	colon:	n/a	n/a
38	POLR2A	chr3:160822331-160823260	MCF-7	breast:	n/a	n/a
39	POLR2A	chr3:160822609-160823113	GM12891	blood:	n/a	n/a
40	POLR2A	chr3:160822687-160823281	HUVEC	blood vessel:	n/a	n/a
41	MAX	chr3:160822407-160823028	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr3:160822546-160823291	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:160822344-160823455	HUVEC	blood vessel:	n/a	n/a
44	ZNF143	chr3:160822294-160823227	H1-hESC	embryonic stem cell:	n/a	chr3:160822502-160822512
45	CTCF	chr3:160822760-160822910	GM12866	blood:	n/a	n/a
46	SIN3A	chr3:160822337-160823305	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:160822320-160822962	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:160822387-160822996	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr3:160822447-160822951	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAF1	chr3:160822292-160823266	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
3	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GALNT1-1	chr3:160822791-160823033	NONHSAT093009

Variant related genes	Relation type
B3GALNT1	TF binding region
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000196542	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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised 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	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3420135	chr3:160821883-160824431	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv877709	chr3:160822198-160826404	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:160821600-160823200	Active TSS	Right Ventricle	heart
2	chr3:160821800-160823200	Active TSS	Left Ventricle	heart
3	chr3:160821800-160823600	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:160821800-160823600	Active TSS	Fetal Brain Female	brain
5	chr3:160821800-160823600	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:160821800-160823800	Active TSS	Brain Substantia Nigra	brain
7	chr3:160821800-160824200	Active TSS	Fetal Kidney	kidney
8	chr3:160822000-160823000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:160822000-160823000	Active TSS	Esophagus	oesophagus
10	chr3:160822000-160823000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:160822000-160823200	Active TSS	Fetal Muscle Trunk	muscle
12	chr3:160822000-160823200	Active TSS	Ovary	ovary
13	chr3:160822000-160823400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:160822000-160823400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:160822000-160823400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:160822000-160823400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:160822000-160823400	Active TSS	Primary T cells from cord blood	blood
18	chr3:160822000-160823400	Active TSS	Muscle Satellite Cultured Cells	--
19	chr3:160822000-160823400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr3:160822000-160823400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:160822000-160823400	Active TSS	Aorta	Aorta
22	chr3:160822000-160823400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:160822000-160823400	Active TSS	Lung	lung
24	chr3:160822000-160823400	Active TSS	Right Atrium	heart
25	chr3:160822000-160823400	Flanking Active TSS	HMEC	breast
26	chr3:160822000-160823600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:160822000-160823600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:160822000-160823600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:160822000-160823600	Active TSS	Brain Angular Gyrus	brain
30	chr3:160822000-160823600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:160822000-160823600	Active TSS	Fetal Brain Male	brain
32	chr3:160822000-160823600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:160822000-160823600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr3:160822000-160823600	Active TSS	NHLF	lung
35	chr3:160822000-160823800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:160822000-160823800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr3:160822200-160822800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:160822200-160822800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:160822200-160822800	Active TSS	Primary B cells from cord blood	blood
40	chr3:160822200-160822800	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr3:160822200-160822800	Active TSS	Fetal Heart	heart
42	chr3:160822200-160822800	Bivalent/Poised TSS	Fetal Thymus	thymus
43	chr3:160822200-160822800	Active TSS	Placenta Amnion	Placenta Amnion
44	chr3:160822200-160822800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr3:160822200-160822800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr3:160822200-160823000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:160822200-160823200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:160822200-160823200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:160822200-160823200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr3:160822200-160823200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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