Variant report

Variant	rs6700723
Chromosome Location	chr1:85514234-85514235
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	USF1	chr1:85514159-85514379	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr1:85514140-85514412	A549	lung:	n/a	n/a
3	EGR1	chr1:85514026-85514433	MCF-7	breast:	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
4	TCF12	chr1:85513969-85514655	ECC-1	luminal epithelium:	n/a	n/a
5	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
6	TCF7L2	chr1:85513843-85514540	HCT-116	colon:	n/a	n/a
7	POLR2A	chr1:85513846-85514536	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr1:85513908-85514571	A549	lung:	n/a	n/a
9	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
10	POLR2A	chr1:85513739-85514516	MCF-7	breast:	n/a	n/a
11	GABPA	chr1:85514071-85514595	MCF-7	breast:	n/a	chr1:85514207-85514216
12	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
13	TCF3	chr1:85513805-85514437	GM12878	blood:	n/a	n/a
14	ZEB1	chr1:85513795-85514599	GM12878	blood:	n/a	n/a
15	EGR1	chr1:85514065-85514362	GM12878	blood:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
16	MAZ	chr1:85514160-85514376	GM12878	blood:	n/a	n/a
17	E2F4	chr1:85514173-85514375	MCF10A-Er-Src	breast:	n/a	chr1:85514220-85514232
18	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
19	BHLHE40	chr1:85514140-85514299	K562	blood:	n/a	n/a
20	EGR1	chr1:85514032-85514339	K562	blood:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
21	POLR2A	chr1:85513838-85514609	ECC-1	luminal epithelium:	n/a	n/a
22	GABPA	chr1:85514171-85514443	GM12878	blood:	n/a	chr1:85514207-85514216
23	ZBTB7A	chr1:85513980-85514445	ECC-1	luminal epithelium:	n/a	n/a
24	BCLAF1	chr1:85514154-85514729	GM12878	blood:	n/a	chr1:85514228-85514237 chr1:85514271-85514280
25	POLR2A	chr1:85513874-85514632	HCT-116	colon:	n/a	n/a
26	NFIC	chr1:85513837-85514625	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr1:85513972-85514429	GM12878	blood:	n/a	n/a
28	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
29	BHLHE40	chr1:85514213-85514306	GM12878	blood:	n/a	n/a
30	BCLAF1	chr1:85513852-85514427	GM12878	blood:	n/a	chr1:85514228-85514237 chr1:85513885-85513894 chr1:85514020-85514033 chr1:85514271-85514280
31	EGR1	chr1:85514060-85514359	K562	blood:	n/a	chr1:85514203-85514225 chr1:85514224-85514237 chr1:85514223-85514238 chr1:85514224-85514237 chr1:85514208-85514221 chr1:85514224-85514234 chr1:85514209-85514220 chr1:85514221-85514235 chr1:85514224-85514237 chr1:85514225-85514234
32	MAX	chr1:85513770-85514584	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr1:85513535-85514652	GM19193	blood:	n/a	n/a
34	POLR2A	chr1:85513876-85514523	GM12892	blood:	n/a	n/a
35	CTCF	chr1:85514120-85514270	GM12864	blood:	n/a	n/a
36	POLR2A	chr1:85513838-85514291	A549	lung:	n/a	n/a
37	NFIC	chr1:85513996-85514721	ECC-1	luminal epithelium:	n/a	n/a
38	ZNF143	chr1:85513984-85514590	GM12878	blood:	n/a	chr1:85514450-85514460 chr1:85514449-85514459 chr1:85514206-85514216
39	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
40	ZBTB7A	chr1:85514039-85514544	ECC-1	luminal epithelium:	n/a	n/a
41	GABPA	chr1:85514128-85514459	A549	lung:	n/a	chr1:85514207-85514216
42	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
43	POLR2A	chr1:85513977-85514432	MCF-7	breast:	n/a	n/a
44	USF1	chr1:85514130-85514389	K562	blood:	n/a	n/a
45	CTCF	chr1:85514137-85514238	GM19238	blood:	n/a	n/a
46	MYC	chr1:85513854-85514417	MCF-7	breast:	n/a	n/a
47	POLR2A	chr1:85514007-85514406	GM12878	blood:	n/a	n/a
48	HMGN3	chr1:85513922-85514243	K562	blood:	n/a	n/a
49	ZNF263	chr1:85513945-85514570	HEK293-T-REx	kidney:	n/a	n/a
50	POLR2A	chr1:85513863-85514535	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85514226-85514276	HCF	heart:	n/a
2	chr1:85514226-85514276	ECC-1	luminal epithelium:	n/a
3	chr1:85514226-85514276	AG04449	skin:	fetal
4	chr1:85514226-85514276	K562	blood:	n/a
5	chr1:85514226-85514276	HCPEpiC	choroid plexus:	n/a
6	chr1:85514226-85514276	HL-60	blood:	n/a
7	chr1:85514226-85514276	NHDF-neo	bronchial:	n/a
8	chr1:85514226-85514276	GM12878	blood:	n/a
9	chr1:85514226-85514276	AG04450	lung:	fetal
10	chr1:85514226-85514276	HNPCEpiC	eye:	n/a
11	chr1:85514226-85514276	AG10803	skin:	n/a
12	chr1:85514226-85514276	SK-N-SH	brain:	n/a
13	chr1:85514226-85514276	HUVEC	blood vessel:	n/a
14	chr1:85514226-85514276	PrEC	prostate:	n/a
15	chr1:85514226-85514276	CMK	blood:	n/a
16	chr1:85514226-85514276	A549	lung:	n/a
17	chr1:85514226-85514276	SAEC	small airway:	n/a
18	chr1:85514226-85514276	HIPEpiC	eye:	n/a
19	chr1:85514226-85514276	HAEpiC	amniotic membrane:	n/a
20	chr1:85514226-85514276	RPTEC	kidney:	n/a
21	chr1:85514226-85514276	BE2_C	brain:	n/a
22	chr1:85514226-85514276	HCT-116	colon:	n/a
23	chr1:85514226-85514276	HEK293	kidney:	embryo
24	chr1:85514226-85514276	NT2-D1	testis:	n/a
25	chr1:85514226-85514276	NH-A	brain:	n/a
26	chr1:85514226-85514276	ovcar-3	ovarian:	n/a
27	chr1:85514226-85514276	AG09309	skin:	n/a
28	chr1:85514226-85514276	Caco-2	colon:	n/a
29	chr1:85514226-85514276	SK-N-MC	brain:	n/a
30	chr1:85514226-85514276	HMEC	breast:	n/a
31	chr1:85514226-85514276	AoSMC	blood vessel:	n/a
32	chr1:85514226-85514276	NB4	blood:	n/a
33	chr1:85514226-85514276	Hela-S3	cervix:	n/a
34	chr1:85514226-85514276	GM06990	blood:	n/a
35	chr1:85514226-85514276	IMR90	lung:	fetal
36	chr1:85514226-85514276	GM12892	blood:	n/a
37	chr1:85514226-85514276	BJ	skin:	n/a
38	chr1:85514226-85514276	SK-N-SH_RA	brain:	n/a
39	chr1:85514226-85514276	T-47D	breast:	n/a
40	chr1:85514226-85514276	GM12891	blood:	n/a
41	chr1:85514226-85514276	PFSK-1	brain:	n/a
42	chr1:85514226-85514276	HRE	kidney:	n/a
43	chr1:85514226-85514276	HRPEpiC	eye:	n/a
44	chr1:85514226-85514276	LNCaP	prostate:	n/a
45	chr1:85514226-85514276	HEEpiC	esophagus:	n/a
46	chr1:85514226-85514276	H1-hESC	embryonic stem cell:	embryo
47	chr1:85514226-85514276	GM19239	blood:	n/a
48	chr1:85514226-85514276	HepG2	liver:	n/a
49	chr1:85514226-85514276	MCF-7	breast:	n/a
50	chr1:85514226-85514276	HRCEpiC	kidney:	n/a

Variant related genes	Relation type
MCOLN3	TF binding region
MCOLN3	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443172	0.84[ASN][1000 genomes]
rs12024977	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028736	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030837	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037219	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12041012	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042160	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028304	0.84[ASN][1000 genomes]
rs2304641	0.99[ASN][1000 genomes]
rs2840050	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61768854	0.93[EUR][1000 genomes]
rs61769366	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61770879	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665436	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679539	0.84[ASN][1000 genomes]
rs6688354	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7522239	0.84[ASN][1000 genomes]
rs7540706	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547224	0.89[EUR][1000 genomes]
rs7547317	0.89[EUR][1000 genomes]
rs893618	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898036	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:116 , 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	chr1:85513000-85514400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:85513000-85514400	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:85513000-85514400	Active TSS	Right Ventricle	heart
7	chr1:85513000-85514600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:85513000-85514800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr1:85513000-85514800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:85513000-85515000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:85513000-85515000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:85513000-85515800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:85513000-85515800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:85513200-85514400	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr1:85513200-85514400	Bivalent/Poised TSS	Osteobl	bone
18	chr1:85513200-85514600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:85513200-85514600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:85513200-85514600	Active TSS	Gastric	stomach
21	chr1:85513200-85514600	Bivalent Enhancer	Spleen	Spleen
22	chr1:85513200-85514800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:85513200-85514800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:85513200-85514800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:85513200-85514800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr1:85513200-85514800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
27	chr1:85513200-85515000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:85513200-85515600	Active TSS	Pancreas	Pancrea
29	chr1:85513200-85515800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr1:85513400-85514400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:85513400-85514400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr1:85513400-85514400	Bivalent/Poised TSS	NHLF	lung
33	chr1:85513400-85514600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:85513400-85514600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:85513400-85514600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85513400-85514600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
37	chr1:85513400-85514600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr1:85513400-85514600	Active TSS	Lung	lung
39	chr1:85513400-85514600	Active TSS	A549	lung
40	chr1:85513400-85514600	Active TSS	NHDF-Ad	bronchial
41	chr1:85513400-85514800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:85513400-85514800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:85513400-85514800	Bivalent/Poised TSS	Thymus	Thymus
44	chr1:85513400-85515000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:85513400-85515200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:85513600-85514400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:85513600-85514400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr1:85513600-85514400	Bivalent/Poised TSS	Left Ventricle	heart
49	chr1:85513600-85514400	Bivalent/Poised TSS	HepG2	liver
50	chr1:85513600-85514400	Active TSS	HMEC	breast

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