Variant report

Variant	rs62055077
Chromosome Location	chr16:73089312-73089313
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	STAT3	chr16:73089248-73089448	MCF10A-Er-Src	breast:	n/a	n/a
2	ARID3A	chr16:73087215-73090250	HepG2	liver:	n/a	chr16:73088864-73088880
3	POLR2A	chr16:73085684-73094561	H1-neurons	neurons:	n/a	n/a
4	CHD2	chr16:73087046-73090226	Hela-S3	cervix:	n/a	chr16:73087450-73087460 chr16:73087960-73087970
5	MAFK	chr16:73088569-73090572	Hela-S3	cervix:	n/a	chr16:73090463-73090478 chr16:73090376-73090391
6	ZKSCAN1	chr16:73089256-73090177	Hela-S3	cervix:	n/a	n/a
7	NR2F2	chr16:73088908-73090042	MCF-7	breast:	n/a	n/a
8	RFX5	chr16:73089280-73089367	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF7L2	chr16:73088745-73089549	MCF-7	breast:	n/a	n/a
10	POLR2A	chr16:73088988-73090646	HepG2	liver:	n/a	n/a
11	TAF1	chr16:73089047-73090867	H1-neurons	neurons:	n/a	n/a
12	FOS	chr16:73089210-73089393	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr16:73089036-73089880	Hela-S3	cervix:	n/a	n/a
14	HDAC2	chr16:73088607-73089847	MCF-7	breast:	n/a	chr16:73088775-73088794 chr16:73089397-73089411 chr16:73088811-73088825 chr16:73088941-73088955 chr16:73089014-73089028 chr16:73088937-73088951 chr16:73088935-73088949 chr16:73088945-73088959 chr16:73089009-73089023 chr16:73088939-73088953 chr16:73088940-73088954
15	RUNX3	chr16:73088544-73089478	GM12878	blood:	n/a	chr16:73089255-73089270 chr16:73088763-73088778
16	HNF4G	chr16:73089252-73090172	HepG2	liver:	n/a	chr16:73089812-73089820
17	STAT3	chr16:73089125-73089325	MCF10A-Er-Src	breast:	n/a	n/a
18	CEBPB	chr16:73088984-73089637	MCF-7	breast:	n/a	n/a
19	POLR2A	chr16:73089061-73090262	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr16:73088440-73091927	MCF10A-Er-Src	breast:	n/a	n/a
21	TAF1	chr16:73089013-73090724	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr16:73089127-73090168	HepG2	liver:	n/a	n/a
23	GTF2F1	chr16:73089097-73090142	Hela-S3	cervix:	n/a	n/a
24	MBD4	chr16:73089220-73090336	HepG2	liver:	n/a	n/a
25	HA-E2F1	chr16:73089236-73089907	MCF-7	breast:	n/a	n/a
26	KAP1	chr16:73089278-73089619	U2OS	brain:	n/a	n/a
27	BHLHE40	chr16:73089253-73090123	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:73086786-73093402	Hela-S3	cervix:	n/a	n/a
29	MAX	chr16:73089154-73090347	Hela-S3	cervix:	n/a	n/a
30	GATA3	chr16:73088505-73090258	MCF-7	breast:	n/a	chr16:73090238-73090249 chr16:73088804-73088815
31	HDAC2	chr16:73089125-73090461	HepG2	liver:	n/a	chr16:73089397-73089411
32	TCF7L2	chr16:73089265-73089843	Hela-S3	cervix:	n/a	n/a
33	TCF7L2	chr16:73088463-73089404	HEK293	kidney:	n/a	n/a
34	RFX5	chr16:73087062-73090234	Hela-S3	cervix:	n/a	chr16:73088319-73088334
35	NFIC	chr16:73089132-73090233	HepG2	liver:	n/a	n/a
36	REST	chr16:73088841-73090994	H1-neurons	neurons:	n/a	n/a
37	MAZ	chr16:73089231-73089750	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr16:73088505-73090282	IMR90	lung:	n/a	n/a
39	SIN3AK20	chr16:73088380-73090195	MCF-7	breast:	n/a	n/a
40	FOXA1	chr16:73088963-73090263	HepG2	liver:	n/a	chr16:73089798-73089810
41	POLR2A	chr16:73086674-73090413	Hela-S3	cervix:	n/a	n/a
42	NFIC	chr16:73088528-73090357	HepG2	liver:	n/a	n/a
43	POLR2A	chr16:73089258-73090284	HepG2	liver:	n/a	n/a
44	POLR2A	chr16:73089136-73092404	MCF10A-Er-Src	breast:	n/a	n/a
45	TCF12	chr16:73086886-73090314	A549	lung:	n/a	n/a
46	TBP	chr16:73088484-73090398	Hela-S3	cervix:	n/a	n/a
47	HEY1	chr16:73088938-73090771	HepG2	liver:	n/a	n/a
48	BRCA1	chr16:73086734-73090278	Hela-S3	cervix:	n/a	chr16:73089202-73089209
49	TEAD4	chr16:73088516-73090463	HepG2	liver:	n/a	n/a
50	CHD1	chr16:73084743-73093728	IMR90	lung:	n/a	chr16:73092049-73092059 chr16:73091379-73091389 chr16:73092358-73092368 chr16:73091670-73091680 chr16:73087450-73087460 chr16:73087960-73087970

No.	Distal block	Cell Line	Cell type
1	chr16:73049519..73050143-chr16:73089033..73089911,2	MCF-7	breast:
2	chr16:73052788..73055370-chr16:73088414..73091315,3	MCF-7	breast:
3	chr16:72820675..72822937-chr16:73088411..73090468,2	MCF-7	breast:
4	chr16:72943044..72944852-chr16:73087640..73090258,2	MCF-7	breast:
5	chr16:73088044..73089636-chr2:188441847..188444162,2	MCF-7	breast:
6	chr16:72963484..72964015-chr16:73089052..73089953,2	MCF-7	breast:
7	chr16:72833626..72835422-chr16:73088428..73090096,2	MCF-7	breast:
8	chr16:72947016..72947886-chr16:73089092..73089868,3	MCF-7	breast:
9	chr16:73088909..73091660-chr16:73169088..73170894,3	MCF-7	breast:
10	chr16:73088393..73091029-chr16:73316559..73318962,2	MCF-7	breast:
11	chr16:73085960..73092476-chr16:73227779..73233499,9	MCF-7	breast:
12	chr16:72695949..72698024-chr16:73089011..73091874,2	MCF-7	breast:
13	chr16:73089132..73092901-chr16:73127629..73131524,4	MCF-7	breast:
14	chr16:72999501..73001518-chr16:73089190..73091983,2	MCF-7	breast:
15	chr16:73046781..73051112-chr16:73086849..73089877,3	MCF-7	breast:
16	chr16:73082425..73084366-chr16:73087319..73089804,2	K562	blood:
17	chr16:73058271..73060863-chr16:73088850..73091395,2	MCF-7	breast:
18	chr16:73018202..73027072-chr16:73088249..73094904,11	MCF-7	breast:
19	chr16:72984070..72988953-chr16:73089098..73093055,6	MCF-7	breast:
20	chr16:73088683..73091239-chr17:62222998..62225387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272250	TF binding region
ENSG00000199753	Chromatin interaction
ENSG00000272330	Chromatin interaction
ENSG00000265573	Chromatin interaction
ENSG00000221799	Chromatin interaction
ENSG00000266402	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs62055069	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62055070	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62055071	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62055072	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62055073	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62055076	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62055081	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62055083	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62055085	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62055087	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62055088	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052905	0.96[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	nsv906898	chr16:73017684-73128146	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv827730	chr16:73066699-73115642	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv827732	chr16:73069343-73116594	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv827733	chr16:73075114-73103721	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1819498	chr16:73079212-73092845	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
6	esv1815924	chr16:73085286-73105415	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:73082600-73090400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr16:73083000-73089600	Enhancers	Fetal Muscle Leg	muscle
3	chr16:73083200-73089600	Enhancers	Fetal Stomach	stomach
4	chr16:73083200-73090600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:73083200-73091000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr16:73083400-73089600	Weak transcription	Right Ventricle	heart
7	chr16:73085800-73091000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr16:73086000-73090000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr16:73086400-73091000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:73086600-73089400	Enhancers	NHDF-Ad	bronchial
11	chr16:73087000-73090800	Enhancers	HMEC	breast
12	chr16:73087200-73089600	Flanking Active TSS	HepG2	liver
13	chr16:73087200-73089800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr16:73087200-73091200	Enhancers	Primary hematopoietic stem cells	blood
15	chr16:73087400-73089400	Enhancers	Stomach Mucosa	stomach
16	chr16:73087600-73089800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr16:73087600-73091400	Weak transcription	Spleen	Spleen
18	chr16:73087800-73089400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr16:73087800-73089400	Enhancers	Duodenum Mucosa	Duodenum
20	chr16:73087800-73089400	Weak transcription	Left Ventricle	heart
21	chr16:73087800-73089600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr16:73087800-73089800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr16:73087800-73090000	Enhancers	Fetal Kidney	kidney
24	chr16:73087800-73090200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:73087800-73090400	Weak transcription	Ovary	ovary
26	chr16:73087800-73090800	Enhancers	Small Intestine	intestine
27	chr16:73087800-73091400	Weak transcription	Lung	lung
28	chr16:73087800-73099200	Active TSS	Aorta	Aorta
29	chr16:73088000-73089400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:73088200-73089800	Flanking Active TSS	Liver	Liver
31	chr16:73088200-73089800	Weak transcription	Brain Substantia Nigra	brain
32	chr16:73088200-73089800	Enhancers	HUVEC	blood vessel
33	chr16:73088200-73091000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr16:73088200-73095200	Active TSS	Right Atrium	heart
35	chr16:73088400-73089800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr16:73088400-73090000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr16:73088400-73090400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr16:73088400-73090600	Bivalent Enhancer	Fetal Thymus	thymus
39	chr16:73088400-73090800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr16:73088400-73090800	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr16:73088400-73091000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:73088400-73091200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:73088400-73091200	Flanking Active TSS	Osteobl	bone
44	chr16:73088600-73089600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:73088600-73090200	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr16:73088600-73090800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr16:73088600-73090800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:73088600-73090800	Flanking Active TSS	Fetal Lung	lung
49	chr16:73088600-73090800	Flanking Active TSS	Hela-S3	cervix
50	chr16:73088600-73091000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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