Variant report

Variant	rs553978914
Chromosome Location	chr16:30346975-30346976
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	POLR2A	chr16:30345508-30346975	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:30346251-30346993	U87	brain:	n/a	n/a
3	POLR2A	chr16:30346310-30347446	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr16:30344992-30347021	GM12892	blood:	n/a	n/a
5	MXI1	chr16:30346525-30347761	HepG2	liver:	n/a	n/a
6	ELF1	chr16:30346306-30346977	GM12878	blood:	n/a	chr16:30346528-30346540 chr16:30346705-30346717 chr16:30346403-30346412 chr16:30346712-30346724 chr16:30346659-30346671
7	SPI1	chr16:30346871-30347151	GM12878	blood:	n/a	n/a
8	EBF1	chr16:30346971-30347180	GM12878	blood:	n/a	n/a
9	MAZ	chr16:30346632-30347598	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:30346007-30346979	Hela-S3	cervix:	n/a	n/a
11	MBD4	chr16:30346836-30348019	HepG2	liver:	n/a	n/a
12	HEY1	chr16:30345511-30348032	HepG2	liver:	n/a	chr16:30346714-30346729
13	HEY1	chr16:30345444-30348016	HepG2	liver:	n/a	chr16:30346714-30346729
14	POLR2A	chr16:30345508-30346984	Hela-S3	cervix:	n/a	n/a
15	REST	chr16:30346836-30347303	A549	lung:	n/a	n/a
16	POLR2A	chr16:30346520-30347972	HepG2	liver:	n/a	n/a
17	PML	chr16:30346284-30347204	GM12878	blood:	n/a	n/a
18	SP1	chr16:30345651-30347037	A549	lung:	n/a	chr16:30346755-30346767 chr16:30346267-30346276 chr16:30346808-30346817 chr16:30346698-30346707 chr16:30346830-30346839 chr16:30346698-30346712 chr16:30346830-30346840 chr16:30346830-30346839 chr16:30346830-30346840 chr16:30346267-30346277 chr16:30346268-30346277 chr16:30346831-30346840 chr16:30346829-30346841 chr16:30346266-30346278 chr16:30346806-30346818 chr16:30346830-30346844 chr16:30346710-30346722 chr16:30346829-30346841 chr16:30346268-30346277 chr16:30346757-30346766 chr16:30346807-30346816 chr16:30346266-30346278 chr16:30346808-30346817 chr16:30346699-30346708 chr16:30346806-30346818 chr16:30346005-30346019
19	SP1	chr16:30345965-30347054	A549	lung:	n/a	chr16:30346755-30346767 chr16:30346267-30346276 chr16:30346808-30346817 chr16:30346698-30346707 chr16:30346830-30346839 chr16:30346698-30346712 chr16:30346830-30346840 chr16:30346830-30346839 chr16:30346830-30346840 chr16:30346267-30346277 chr16:30346268-30346277 chr16:30346831-30346840 chr16:30346829-30346841 chr16:30346266-30346278 chr16:30346806-30346818 chr16:30346830-30346844 chr16:30346710-30346722 chr16:30346829-30346841 chr16:30346268-30346277 chr16:30346757-30346766 chr16:30346807-30346816 chr16:30346266-30346278 chr16:30346808-30346817 chr16:30346699-30346708 chr16:30346806-30346818 chr16:30346005-30346019
20	POLR2A	chr16:30345909-30347118	U87	brain:	n/a	n/a
21	TFAP2A	chr16:30345849-30347236	Hela-S3	cervix:	n/a	chr16:30346080-30346088 chr16:30346710-30346725 chr16:30346079-30346094 chr16:30346532-30346544 chr16:30346443-30346451 chr16:30346061-30346069 chr16:30346243-30346253 chr16:30346062-30346070 chr16:30346443-30346451 chr16:30346062-30346070 chr16:30346241-30346255 chr16:30346532-30346544 chr16:30346080-30346088 chr16:30346061-30346069 chr16:30346842-30346856 chr16:30346532-30346544 chr16:30346243-30346253 chr16:30346062-30346070 chr16:30346243-30346253 chr16:30346778-30346790 chr16:30346080-30346088 chr16:30346061-30346069 chr16:30346532-30346544 chr16:30346443-30346451
22	SP1	chr16:30344914-30347031	HepG2	liver:	n/a	chr16:30346755-30346767 chr16:30346267-30346276 chr16:30346808-30346817 chr16:30346698-30346707 chr16:30346830-30346839 chr16:30346698-30346712 chr16:30346830-30346840 chr16:30346830-30346839 chr16:30346830-30346840 chr16:30346267-30346277 chr16:30346268-30346277 chr16:30346831-30346840 chr16:30346829-30346841 chr16:30346266-30346278 chr16:30346806-30346818 chr16:30346830-30346844 chr16:30346710-30346722 chr16:30346829-30346841 chr16:30346268-30346277 chr16:30346757-30346766 chr16:30346807-30346816 chr16:30346266-30346278 chr16:30346808-30346817 chr16:30346699-30346708 chr16:30346806-30346818 chr16:30346005-30346019
23	RXRA	chr16:30346042-30346994	HepG2	liver:	n/a	n/a
24	ZNF384	chr16:30346820-30347228	GM12878	blood:	n/a	n/a
25	MAX	chr16:30346380-30346993	K562	blood:	n/a	n/a
26	TFAP2C	chr16:30345896-30347232	Hela-S3	cervix:	n/a	chr16:30346529-30346544 chr16:30346840-30346855
27	POLR2A	chr16:30346458-30347001	NB4	blood:	n/a	n/a
28	POLR2A	chr16:30345126-30346987	GM12892	blood:	n/a	n/a
29	POLR2A	chr16:30346471-30347700	HepG2	liver:	n/a	n/a
30	POLR2A	chr16:30345634-30347040	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr16:30346007-30348661	HepG2	liver:	n/a	n/a
32	POLR2A	chr16:30345564-30347001	HepG2	liver:	n/a	n/a
33	REST	chr16:30346436-30347830	HepG2	liver:	n/a	chr16:30347307-30347327 chr16:30347307-30347327 chr16:30347313-30347327
34	POLR2A	chr16:30345675-30347109	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr16:30345991-30347006	GM18951	blood:	n/a	n/a
36	SP1	chr16:30345440-30346978	GM12878	blood:	n/a	chr16:30346755-30346767 chr16:30346267-30346276 chr16:30346808-30346817 chr16:30346698-30346707 chr16:30346830-30346839 chr16:30346698-30346712 chr16:30346830-30346840 chr16:30346830-30346839 chr16:30346830-30346840 chr16:30346267-30346277 chr16:30346268-30346277 chr16:30346831-30346840 chr16:30346829-30346841 chr16:30346266-30346278 chr16:30346806-30346818 chr16:30346830-30346844 chr16:30346710-30346722 chr16:30346829-30346841 chr16:30346268-30346277 chr16:30346757-30346766 chr16:30346807-30346816 chr16:30346266-30346278 chr16:30346808-30346817 chr16:30346699-30346708 chr16:30346806-30346818 chr16:30346005-30346019
37	TAF1	chr16:30345541-30347027	HepG2	liver:	n/a	n/a
38	POLR2A	chr16:30345643-30347961	HepG2	liver:	n/a	n/a
39	POLR2A	chr16:30346033-30346990	MCF-7	breast:	n/a	n/a
40	MXI1	chr16:30346536-30347009	GM12878	blood:	n/a	n/a
41	TCF12	chr16:30346389-30347246	A549	lung:	n/a	chr16:30347211-30347221
42	POLR2A	chr16:30345530-30347136	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr16:30345026-30347346	GM12878	blood:	n/a	n/a
44	RUNX3	chr16:30346899-30347421	GM12878	blood:	n/a	chr16:30347335-30347350
45	POLR2A	chr16:30345032-30346997	H1-hESC	embryonic stem cell:	n/a	n/a
46	EBF1	chr16:30346669-30347305	GM12878	blood:	n/a	n/a
47	POLR2A	chr16:30346496-30347859	HepG2	liver:	n/a	n/a
48	GABPA	chr16:30346865-30347312	A549	lung:	n/a	n/a
49	MAX	chr16:30346553-30347237	Hela-S3	cervix:	n/a	n/a
50	MAZ	chr16:30345740-30347453	IMR90	lung:	n/a	chr16:30345880-30345889 chr16:30345879-30345890 chr16:30345992-30346002

No.	Distal block	Cell Line	Cell type
1	chr16:30346820..30348778-chr16:30708252..30710060,2	K562	blood:
2	chr16:30345231..30348064-chr16:30583285..30585199,2	MCF-7	breast:
3	chr16:30346170..30348596-chr16:30376800..30378752,2	MCF-7	breast:
4	chr16:30346222..30347053-chr6:2999778..3000588,2	Hela-S3	cervix:
5	chr16:30345604..30348863-chr16:30403977..30407853,5	MCF-7	breast:
6	chr16:30345336..30346987-chr16:30364992..30366777,2	K562	blood:
7	chr16:30345346..30347194-chr16:30364689..30366452,2	MCF-7	breast:
8	chr16:30344696..30347636-chr16:30378058..30380333,2	MCF-7	breast:
9	chr16:30345814..30348548-chr16:30669791..30672071,2	MCF-7	breast:
10	chr12:56211453..56212433-chr16:30346609..30347165,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000183604	TF binding region
ENSG00000169221	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000229809	Chromatin interaction
ENSG00000080603	Chromatin interaction
ENSG00000124588	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000239791	Chromatin interaction
ENSG00000180096	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061165	chr16:29657389-30363743	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking 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	229 gene(s)	inside rSNPs	diseases
4	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
6	esv1829730	chr16:30192562-30359312	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv978131	chr16:30269117-30347376	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3439168	chr16:30345276-30348024	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30344000-30347000	Active TSS	GM12878-XiMat	blood
2	chr16:30344000-30347000	Active TSS	NHEK	skin
3	chr16:30344200-30347600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:30344400-30347000	Weak transcription	Fetal Heart	heart
5	chr16:30344400-30347000	Active TSS	Hela-S3	cervix
6	chr16:30344400-30347000	Active TSS	HSMMtube	muscle
7	chr16:30344400-30347000	Active TSS	K562	blood
8	chr16:30344400-30347200	Active TSS	HepG2	liver
9	chr16:30344600-30347000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr16:30344600-30347000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr16:30344600-30347000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:30344600-30347000	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr16:30344600-30347000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:30344600-30347000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr16:30344600-30347200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr16:30344600-30347200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr16:30344600-30347200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:30344600-30347200	Active TSS	HMEC	breast
19	chr16:30344600-30347400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr16:30344800-30347000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:30344800-30347000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:30344800-30347000	Active TSS	HUVEC	blood vessel
23	chr16:30344800-30347400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:30344800-30347600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:30345200-30347000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:30345200-30347000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr16:30345200-30347000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr16:30345200-30347000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr16:30345200-30347000	Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr16:30345200-30347000	Active TSS	Muscle Satellite Cultured Cells	--
31	chr16:30345200-30347000	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr16:30345200-30347000	Active TSS	Duodenum Mucosa	Duodenum
33	chr16:30345200-30347000	Active TSS	Fetal Intestine Small	intestine
34	chr16:30345200-30347000	Active TSS	Fetal Lung	lung
35	chr16:30345200-30347000	Active TSS	Fetal Muscle Leg	muscle
36	chr16:30345200-30347000	Active TSS	A549	lung
37	chr16:30345200-30347200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:30345200-30347200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:30345200-30347200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr16:30345200-30347200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr16:30345200-30347200	Active TSS	Psoas Muscle	Psoas
42	chr16:30345200-30347200	Active TSS	Right Atrium	heart
43	chr16:30345200-30347200	Active TSS	Right Ventricle	heart
44	chr16:30345200-30347200	Active TSS	NHDF-Ad	bronchial
45	chr16:30345200-30347200	Active TSS	NHLF	lung
46	chr16:30345200-30347400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr16:30345400-30347000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr16:30345400-30347000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:30345400-30347000	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr16:30345400-30347000	Active TSS	Primary B cells from peripheral blood	blood

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