Variant report

Variant	rs562814726
Chromosome Location	chr1:85514457-85514458
allele	-/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	CTCF	chr1:85514400-85514581	GM13977	blood:	n/a	chr1:85514462-85514480
2	TCF12	chr1:85513969-85514655	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr1:85513866-85514658	ECC-1	luminal epithelium:	n/a	chr1:85514372-85514385 chr1:85514207-85514216 chr1:85513877-85513893 chr1:85514024-85514033 chr1:85514449-85514458 chr1:85514443-85514459 chr1:85513884-85513893 chr1:85514499-85514515
4	TCF7L2	chr1:85513843-85514540	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:85513846-85514536	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr1:85514441-85514618	GM19238	blood:	n/a	chr1:85514462-85514480
7	MAX	chr1:85513908-85514571	A549	lung:	n/a	n/a
8	YY1	chr1:85513744-85514579	GM12892	blood:	n/a	chr1:85513944-85513958 chr1:85514446-85514460 chr1:85514058-85514072 chr1:85514226-85514237 chr1:85513784-85513793 chr1:85514449-85514463 chr1:85514226-85514235 chr1:85514199-85514213 chr1:85513826-85513837 chr1:85513887-85513896 chr1:85514443-85514457 chr1:85513884-85513893
9	POLR2A	chr1:85513739-85514516	MCF-7	breast:	n/a	n/a
10	GABPA	chr1:85514071-85514595	MCF-7	breast:	n/a	chr1:85514207-85514216
11	YY1	chr1:85514093-85514559	HCT-116	colon:	n/a	chr1:85514446-85514460 chr1:85514226-85514237 chr1:85514449-85514463 chr1:85514226-85514235 chr1:85514199-85514213 chr1:85514443-85514457
12	ZEB1	chr1:85513795-85514599	GM12878	blood:	n/a	n/a
13	CTCF	chr1:85514380-85514530	GM12870	blood:	n/a	chr1:85514462-85514480
14	EP300	chr1:85514027-85514518	ECC-1	luminal epithelium:	n/a	chr1:85514372-85514385 chr1:85514207-85514216 chr1:85514449-85514458 chr1:85514443-85514459 chr1:85514499-85514515
15	POLR2A	chr1:85513838-85514609	ECC-1	luminal epithelium:	n/a	n/a
16	RUNX3	chr1:85514331-85514710	GM12878	blood:	n/a	n/a
17	BCLAF1	chr1:85514154-85514729	GM12878	blood:	n/a	chr1:85514228-85514237 chr1:85514271-85514280
18	POLR2A	chr1:85513874-85514632	HCT-116	colon:	n/a	n/a
19	KAP1	chr1:85514407-85514736	HEK293	kidney:	n/a	n/a
20	CTCF	chr1:85514410-85514616	K562	blood:	n/a	chr1:85514462-85514480
21	NFIC	chr1:85513837-85514625	ECC-1	luminal epithelium:	n/a	n/a
22	EGR1	chr1:85514017-85514480	ECC-1	luminal epithelium:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514360-85514370 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
23	MAX	chr1:85513770-85514584	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr1:85513535-85514652	GM19193	blood:	n/a	n/a
25	POLR2A	chr1:85513876-85514523	GM12892	blood:	n/a	n/a
26	NFIC	chr1:85513996-85514721	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr1:85514400-85514550	GM06990	blood:	n/a	chr1:85514462-85514480
28	ZNF143	chr1:85513984-85514590	GM12878	blood:	n/a	chr1:85514450-85514460 chr1:85514449-85514459 chr1:85514206-85514216
29	EGR1	chr1:85513872-85514806	HCT-116	colon:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514360-85514370 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234 chr1:85513879-85513892
30	ZBTB7A	chr1:85514039-85514544	ECC-1	luminal epithelium:	n/a	n/a
31	GABPA	chr1:85514128-85514459	A549	lung:	n/a	chr1:85514207-85514216
32	YY1	chr1:85513788-85514483	ECC-1	luminal epithelium:	n/a	chr1:85513944-85513958 chr1:85514446-85514460 chr1:85514058-85514072 chr1:85514226-85514237 chr1:85514449-85514463 chr1:85514226-85514235 chr1:85514199-85514213 chr1:85513826-85513837 chr1:85513887-85513896 chr1:85514443-85514457 chr1:85513884-85513893
33	ZNF263	chr1:85513945-85514570	HEK293-T-REx	kidney:	n/a	n/a
34	POLR2A	chr1:85513863-85514535	HCT-116	colon:	n/a	n/a
35	TAF1	chr1:85513788-85514514	ECC-1	luminal epithelium:	n/a	n/a
36	NANOG	chr1:85513869-85514463	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIN3AK20	chr1:85513808-85514610	PANC-1	pancreas:	n/a	n/a
38	USF1	chr1:85514045-85514463	ECC-1	luminal epithelium:	n/a	chr1:85514441-85514457 chr1:85514447-85514463 chr1:85514444-85514460 chr1:85514438-85514454
39	TEAD4	chr1:85514052-85514462	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:85513857-85514653	GM15510	blood:	n/a	n/a
41	TEAD4	chr1:85514039-85514533	ECC-1	luminal epithelium:	n/a	n/a
42	EGR1	chr1:85514019-85514711	HCT-116	colon:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514360-85514370 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
43	EGR1	chr1:85514031-85514514	ECC-1	luminal epithelium:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514360-85514370 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
44	CTCF	chr1:85514360-85514510	GM12873	blood:	n/a	chr1:85514462-85514480
45	CTCF	chr1:85514360-85514510	HRE	kidney:	n/a	chr1:85514462-85514480
46	TCF12	chr1:85514095-85514762	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr1:85513557-85514615	GM18951	blood:	n/a	n/a
48	EGR1	chr1:85513983-85514464	H1-hESC	embryonic stem cell:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514360-85514370 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
49	POU2F2	chr1:85514366-85514728	GM12891	blood:	n/a	chr1:85514571-85514589 chr1:85514575-85514584 chr1:85514576-85514584
50	ELF1	chr1:85513328-85514648	GM12878	blood:	n/a	chr1:85514222-85514234 chr1:85514255-85514267 chr1:85513536-85513548 chr1:85514450-85514462

Variant related genes	Relation type
MCOLN3	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	esv3448123	chr1:85513114-85515312	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85512400-85515800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:85512800-85514600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
3	chr1:85512800-85514800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
4	chr1:85513000-85514600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:85513000-85514800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr1:85513000-85514800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:85513000-85515000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:85513000-85515000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:85513000-85515800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:85513000-85515800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:85513200-85514600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr1:85513200-85514600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:85513200-85514600	Active TSS	Gastric	stomach
16	chr1:85513200-85514600	Bivalent Enhancer	Spleen	Spleen
17	chr1:85513200-85514800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:85513200-85514800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:85513200-85514800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:85513200-85514800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr1:85513200-85514800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr1:85513200-85515000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:85513200-85515600	Active TSS	Pancreas	Pancrea
24	chr1:85513200-85515800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr1:85513400-85514600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:85513400-85514600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:85513400-85514600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:85513400-85514600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr1:85513400-85514600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
30	chr1:85513400-85514600	Active TSS	Lung	lung
31	chr1:85513400-85514600	Active TSS	A549	lung
32	chr1:85513400-85514600	Active TSS	NHDF-Ad	bronchial
33	chr1:85513400-85514800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:85513400-85514800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:85513400-85514800	Bivalent/Poised TSS	Thymus	Thymus
36	chr1:85513400-85515000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr1:85513400-85515200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:85513600-85514600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:85513600-85514600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr1:85513600-85514600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
41	chr1:85513600-85514600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr1:85513600-85514600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:85513600-85514600	Enhancers	Liver	Liver
44	chr1:85513600-85514600	Bivalent/Poised TSS	Esophagus	oesophagus
45	chr1:85513600-85514600	Bivalent/Poised TSS	HSMM	muscle
46	chr1:85513600-85514600	Bivalent/Poised TSS	NH-A	brain
47	chr1:85513600-85514800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:85513600-85514800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr1:85513600-85514800	Active TSS	Aorta	Aorta
50	chr1:85513600-85514800	Bivalent/Poised TSS	NHEK	skin

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