Variant report

Variant	rs536060057
Chromosome Location	chr5:179780258-179780259
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	REST	chr5:179779518-179781067	H1-neurons	neurons:	n/a	chr5:179780129-179780142 chr5:179779998-179780011
2	POLR2A	chr5:179779802-179780885	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr5:179780115-179780912	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr5:179780104-179781007	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179780079-179780754	HEK293	kidney:	n/a	n/a
6	MXI1	chr5:179779162-179781150	SK-N-SH	brain:	n/a	chr5:179780445-179780460 chr5:179780447-179780462
7	POLR2A	chr5:179779887-179780778	U87	brain:	n/a	n/a
8	MAX	chr5:179779075-179781088	A549	lung:	n/a	chr5:179780484-179780494 chr5:179780417-179780427
9	POLR2A	chr5:179780071-179780474	A549	lung:	n/a	n/a
10	POLR2A	chr5:179780102-179780353	A549	lung:	n/a	n/a
11	POLR2A	chr5:179779403-179780696	IMR90	lung:	n/a	n/a
12	POLR2A	chr5:179779968-179780974	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr5:179780133-179780413	MCF10A-Er-Src	breast:	n/a	n/a
14	SIN3A	chr5:179778620-179780906	H1-hESC	embryonic stem cell:	n/a	chr5:179780060-179780073 chr5:179780035-179780046
15	SP1	chr5:179780214-179780728	H1-hESC	embryonic stem cell:	n/a	chr5:179780423-179780444
16	BACH1	chr5:179779932-179780969	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr5:179780080-179780355	Hela-S3	cervix:	n/a	n/a
18	NFYB	chr5:179780102-179780719	K562	blood:	n/a	chr5:179780430-179780445 chr5:179780430-179780445 chr5:179780432-179780447 chr5:179780431-179780445
19	CCNT2	chr5:179779882-179780557	K562	blood:	n/a	n/a
20	POLR2A	chr5:179780131-179780342	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr5:179780092-179780390	A549	lung:	n/a	n/a
22	TAF1	chr5:179780015-179780366	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr5:179780027-179780462	Hela-S3	cervix:	n/a	n/a
24	SMARCB1	chr5:179779451-179780305	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:179779980-179780434	U87	brain:	n/a	n/a
26	NFYB	chr5:179780254-179780564	GM12878	blood:	n/a	chr5:179780430-179780445 chr5:179780430-179780445 chr5:179780432-179780447 chr5:179780431-179780445
27	MXI1	chr5:179778505-179781093	IMR90	lung:	n/a	chr5:179780445-179780460 chr5:179780447-179780462
28	POLR2A	chr5:179780092-179780340	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:179780066-179780707	HCT-116	colon:	n/a	n/a
30	TBP	chr5:179780212-179780575	K562	blood:	n/a	n/a
31	POLR2A	chr5:179780094-179780670	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr5:179779499-179780668	H1-hESC	embryonic stem cell:	n/a	n/a
33	RCOR1	chr5:179779372-179781018	IMR90	lung:	n/a	n/a
34	CTCF	chr5:179780060-179780290	AG04449	skin:	n/a	chr5:179780119-179780132
35	POLR2A	chr5:179779876-179780738	A549	lung:	n/a	n/a
36	MAZ	chr5:179778623-179781035	IMR90	lung:	n/a	chr5:179780484-179780494 chr5:179780417-179780427
37	POLR2A	chr5:179780004-179780462	ProgFib	skin:	n/a	n/a
38	POLR2A	chr5:179780094-179780399	A549	lung:	n/a	n/a
39	POLR2A	chr5:179779816-179780654	MCF-7	breast:	n/a	n/a
40	POLR2A	chr5:179780011-179780991	H1-neurons	neurons:	n/a	n/a
41	TBP	chr5:179780178-179780446	Hela-S3	cervix:	n/a	n/a
42	E2F6	chr5:179780108-179780268	K562	blood:	n/a	chr5:179780135-179780144 chr5:179780194-179780203 chr5:179780152-179780162
43	POLR2A	chr5:179780057-179780386	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr5:179780044-179780453	MCF-7	breast:	n/a	n/a
45	POLR2A	chr5:179780090-179780443	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr5:179780120-179780468	MCF-7	breast:	n/a	n/a
47	POLR2A	chr5:179780059-179780380	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr5:179780053-179780668	HCT-116	colon:	n/a	n/a
49	POLR2A	chr5:179779942-179780433	U87	brain:	n/a	n/a
50	SP4	chr5:179780248-179780622	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179778332..179781251-chr5:179920436..179923318,3	MCF-7	breast:
2	chr5:179758118..179760214-chr5:179779421..179781494,2	MCF-7	breast:

Variant related genes	Relation type
GFPT2	TF binding region
ENSG00000113300	Chromatin interaction
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
5	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
9	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
10	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
11	nsv883291	chr5:179755559-179818868	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv984575	chr5:179759624-179791220	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv3327832	chr5:179779171-179781719	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179777800-179780600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr5:179777800-179781800	Enhancers	Fetal Heart	heart
3	chr5:179778000-179781400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:179778200-179780600	Active TSS	Colon Smooth Muscle	Colon
5	chr5:179778400-179780600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:179778400-179780600	Bivalent Enhancer	Fetal Brain Male	brain
7	chr5:179778600-179780600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:179778800-179780600	Active TSS	Left Ventricle	heart
9	chr5:179778800-179781400	Active TSS	Right Atrium	heart
10	chr5:179779000-179780600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:179779000-179780600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:179779000-179780600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr5:179779000-179781000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
14	chr5:179779000-179781000	Active TSS	NHDF-Ad	bronchial
15	chr5:179779000-179781200	Bivalent/Poised TSS	Psoas Muscle	Psoas
16	chr5:179779000-179781400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:179779000-179781400	Active TSS	Brain Angular Gyrus	brain
18	chr5:179779200-179780600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr5:179779200-179780600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:179779200-179780600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:179779200-179780600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr5:179779200-179780600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:179779200-179780600	Active TSS	Brain Substantia Nigra	brain
24	chr5:179779200-179780600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr5:179779200-179780600	Active TSS	NH-A	brain
26	chr5:179779200-179781000	Active TSS	Fetal Kidney	kidney
27	chr5:179779200-179781000	Active TSS	A549	lung
28	chr5:179779200-179781000	Active TSS	Hela-S3	cervix
29	chr5:179779200-179781000	Active TSS	HSMM	muscle
30	chr5:179779200-179781000	Active TSS	HSMMtube	muscle
31	chr5:179779200-179781200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr5:179779200-179781200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:179779200-179781200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:179779200-179781200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:179779200-179781200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:179779200-179781200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:179779200-179781200	Active TSS	Brain Cingulate Gyrus	brain
38	chr5:179779200-179781400	Active TSS	Ovary	ovary
39	chr5:179779200-179781800	Active TSS	Brain Anterior Caudate	brain
40	chr5:179779200-179781800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:179779400-179780400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:179779400-179780400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:179779400-179780400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
44	chr5:179779400-179780400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr5:179779400-179780600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:179779400-179780600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:179779400-179780600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:179779400-179780600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:179779400-179780600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:179779400-179780600	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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