Variant report

Variant	rs139159699
Chromosome Location	chr3:178789991-178789992
allele	C/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	SPI1	chr3:178789918-178790091	GM12878	blood:	n/a	chr3:178790040-178790053
2	ZNF143	chr3:178788908-178790072	GM12878	blood:	n/a	chr3:178789152-178789170
3	POLR2A	chr3:178788718-178790508	GM12878	blood:	n/a	n/a
4	ELF1	chr3:178789318-178790210	HepG2	liver:	n/a	chr3:178789678-178789687 chr3:178790046-178790059 chr3:178789504-178789516
5	ELK1	chr3:178789217-178790201	GM12878	blood:	n/a	n/a
6	EGR1	chr3:178789985-178790234	GM12878	blood:	n/a	chr3:178790141-178790155 chr3:178790119-178790134 chr3:178790121-178790135 chr3:178790047-178790056
7	POLR2A	chr3:178788597-178790407	GM18505	blood:	n/a	n/a
8	JUND	chr3:178788802-178790289	K562	blood:	n/a	chr3:178789723-178789732
9	MAX	chr3:178788899-178790200	HepG2	liver:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
10	POLR2A	chr3:178789286-178790065	PANC-1	pancreas:	n/a	n/a
11	MXI1	chr3:178787729-178790159	IMR90	lung:	n/a	n/a
12	NFATC1	chr3:178788862-178790387	GM12878	blood:	n/a	n/a
13	MAX	chr3:178788868-178790192	HCT-116	colon:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
14	POLR2A	chr3:178789266-178790383	K562	blood:	n/a	n/a
15	POLR2A	chr3:178789090-178790361	K562	blood:	n/a	n/a
16	POLR2A	chr3:178788869-178790435	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:178789288-178790064	Hela-S3	cervix:	n/a	n/a
18	MAX	chr3:178788878-178790157	ECC-1	luminal epithelium:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
19	POLR2A	chr3:178788832-178790483	GM12892	blood:	n/a	n/a
20	GABPA	chr3:178789008-178790022	SK-N-SH	brain:	n/a	chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789651-178789665
21	POLR2A	chr3:178788899-178790390	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:178788918-178790493	GM19193	blood:	n/a	n/a
23	POLR2A	chr3:178788980-178790289	GM15510	blood:	n/a	n/a
24	SPI1	chr3:178789838-178790245	HL-60	blood:	n/a	chr3:178790040-178790053
25	POLR2A	chr3:178788923-178790330	GM18526	blood:	n/a	n/a
26	POLR2A	chr3:178789275-178789999	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr3:178788908-178790352	GM18951	blood:	n/a	n/a
28	USF2	chr3:178789025-178790057	GM12878	blood:	n/a	chr3:178789275-178789286 chr3:178789680-178789696 chr3:178789719-178789735
29	TBL1XR1	chr3:178788901-178790105	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:178788967-178790444	GM12892	blood:	n/a	n/a
31	MTA3	chr3:178788765-178790429	GM12878	blood:	n/a	n/a
32	PML	chr3:178789414-178789995	MCF-7	breast:	n/a	n/a
33	POLR2A	chr3:178789354-178789991	U87	brain:	n/a	n/a
34	SMARCB1	chr3:178789034-178790199	Hela-S3	cervix:	n/a	n/a
35	RUNX3	chr3:178788861-178790226	GM12878	blood:	n/a	chr3:178789979-178789996
36	POLR2A	chr3:178789097-178790150	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:178787857-178790057	IMR90	lung:	n/a	n/a
38	ATF2	chr3:178789396-178790175	GM12878	blood:	n/a	n/a
39	CTBP2	chr3:178789007-178790005	H1-hESC	embryonic stem cell:	n/a	n/a
40	GABPA	chr3:178788979-178789995	MCF-7	breast:	n/a	chr3:178789654-178789665 chr3:178789654-178789663 chr3:178789724-178789733 chr3:178789765-178789774 chr3:178789651-178789665
41	POLR2A	chr3:178789307-178789991	U87	brain:	n/a	n/a
42	GTF2F1	chr3:178789236-178790032	K562	blood:	n/a	n/a
43	POLR2A	chr3:178789014-178790304	ProgFib	skin:	n/a	n/a
44	POLR2A	chr3:178788824-178790459	GM12891	blood:	n/a	n/a
45	POLR2A	chr3:178788886-178790187	Hela-S3	cervix:	n/a	n/a
46	MAX	chr3:178788872-178790171	A549	lung:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
47	ELF1	chr3:178789241-178790214	K562	blood:	n/a	chr3:178789678-178789687 chr3:178790046-178790059 chr3:178789504-178789516
48	POLR2A	chr3:178789156-178790062	Gliobla	brain:	n/a	n/a
49	MAX	chr3:178788978-178790017	H1-hESC	embryonic stem cell:	n/a	chr3:178789279-178789295 chr3:178789808-178789818 chr3:178789656-178789666
50	POLR2A	chr3:178789170-178790253	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178788412..178790187-chr3:179039067..179041157,2	MCF-7	breast:
2	chr3:178787120..178791261-chr3:179039253..179041998,3	K562	blood:
3	chr3:178788594..178790647-chr3:179063924..179066564,2	K562	blood:
4	chr3:178787966..178791118-chr3:178865051..178866959,3	MCF-7	breast:
5	chr3:178788554..178791044-chr3:178814072..178816691,3	MCF-7	breast:
6	chr3:178786925..178790579-chr3:178864297..178867679,5	K562	blood:
7	chr3:178788447..178791036-chr3:178864497..178866649,2	MCF-7	breast:
8	chr3:178787982..178790546-chr3:179037129..179041546,5	MCF-7	breast:

Variant related genes	Relation type
ZMAT3	TF binding region
ENSG00000171109	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000200616	Chromatin interaction
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3325944	chr3:178788483-178791031	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178785600-178790000	Active TSS	GM12878-XiMat	blood
2	chr3:178786600-178790200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:178787000-178790000	Active TSS	NHDF-Ad	bronchial
4	chr3:178787000-178790200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:178787000-178790200	Active TSS	HSMMtube	muscle
6	chr3:178787000-178790400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:178787200-178790200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:178787200-178790200	Active TSS	NHLF	lung
9	chr3:178787200-178790400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:178787400-178790000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:178787400-178790200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:178787400-178790200	Active TSS	Thymus	Thymus
13	chr3:178787400-178790400	Active TSS	A549	lung
14	chr3:178787600-178790200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:178787600-178790400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:178787800-178790200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:178787800-178790200	Active TSS	Aorta	Aorta
18	chr3:178787800-178790200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:178787800-178790400	Active TSS	Brain Hippocampus Middle	brain
20	chr3:178788000-178790400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:178788000-178790400	Active TSS	Brain Substantia Nigra	brain
22	chr3:178788200-178790400	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:178788200-178790400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:178788400-178790000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:178788400-178790000	Active TSS	Stomach Mucosa	stomach
26	chr3:178788400-178790200	Active TSS	H9 Cell Line	embryonic stem cell
27	chr3:178788400-178790200	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:178788400-178790400	Active TSS	Colonic Mucosa	Colon
29	chr3:178788400-178790400	Active TSS	Colon Smooth Muscle	Colon
30	chr3:178788400-178790400	Active TSS	Right Atrium	heart
31	chr3:178788600-178790000	Bivalent/Poised TSS	HepG2	liver
32	chr3:178788600-178790200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:178788600-178790200	Active TSS	Right Ventricle	heart
34	chr3:178788600-178790400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:178788600-178790400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr3:178788800-178790000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr3:178788800-178790000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:178788800-178790000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:178788800-178790000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:178788800-178790000	Active TSS	Fetal Heart	heart
41	chr3:178788800-178790000	Active TSS	Fetal Muscle Trunk	muscle
42	chr3:178788800-178790000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:178788800-178790000	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr3:178788800-178790200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr3:178788800-178790200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:178788800-178790200	Active TSS	Brain Angular Gyrus	brain
47	chr3:178788800-178790200	Active TSS	Brain Anterior Caudate	brain
48	chr3:178788800-178790200	Active TSS	Duodenum Mucosa	Duodenum
49	chr3:178788800-178790200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:178788800-178790200	Active TSS	Esophagus	oesophagus

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