Variant report

Variant	rs16996065
Chromosome Location	chr4:87857813-87857814
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	FOXM1	chr4:87856979-87857995	GM12878	blood:	n/a	n/a
2	TCF7L2	chr4:87857182-87857987	PANC-1	pancreas:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
3	RAD21	chr4:87857484-87857813	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:87855390-87857870	GM12878	blood:	n/a	n/a
5	CUX1	chr4:87857125-87858337	K562	blood:	n/a	n/a
6	MAZ	chr4:87857118-87857836	HepG2	liver:	n/a	n/a
7	CREB1	chr4:87856798-87857965	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:87855397-87857921	GM19099	blood:	n/a	n/a
9	TCF7L2	chr4:87856233-87857994	Hela-S3	cervix:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
10	HNF4G	chr4:87857352-87857915	HepG2	liver:	n/a	chr4:87857707-87857719 chr4:87857706-87857721 chr4:87857707-87857719 chr4:87857705-87857720 chr4:87857706-87857720
11	HCFC1	chr4:87855249-87857912	K562	blood:	n/a	n/a
12	SMC3	chr4:87856810-87857825	Hela-S3	cervix:	n/a	n/a
13	ZNF384	chr4:87857130-87858070	K562	blood:	n/a	n/a
14	SIN3A	chr4:87857054-87857961	GM12878	blood:	n/a	n/a
15	CTCF	chr4:87857307-87857867	K562	blood:	n/a	n/a
16	HDAC2	chr4:87857360-87858017	HepG2	liver:	n/a	chr4:87857728-87857742
17	POLR2A	chr4:87855314-87857869	NB4	blood:	n/a	n/a
18	SP1	chr4:87857148-87857979	A549	lung:	n/a	n/a
19	POLR2A	chr4:87856064-87857845	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:87855525-87857861	GM12892	blood:	n/a	n/a
21	CTCF	chr4:87857059-87857853	GM12878	blood:	n/a	n/a
22	MAFK	chr4:87857088-87857901	HepG2	liver:	n/a	n/a
23	ZNF143	chr4:87856676-87857887	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:87855428-87858463	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr4:87857336-87857906	GM12878	blood:	n/a	n/a
26	SMC3	chr4:87857111-87857982	GM12878	blood:	n/a	n/a
27	EP300	chr4:87857176-87857994	HepG2	liver:	n/a	chr4:87857855-87857862
28	CEBPB	chr4:87857084-87858012	GM12878	blood:	n/a	n/a
29	MAX	chr4:87855356-87857880	Hela-S3	cervix:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
30	RAD21	chr4:87857356-87857900	GM12878	blood:	n/a	n/a
31	MBD4	chr4:87857024-87858026	HepG2	liver:	n/a	n/a
32	CBX3	chr4:87856993-87857925	K562	blood:	n/a	n/a
33	POLR2A	chr4:87856667-87857933	HepG2	liver:	n/a	n/a
34	MYC	chr4:87855279-87858209	K562	blood:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
35	JUND	chr4:87856996-87857889	HepG2	liver:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857424-87857433 chr4:87857422-87857433
36	POLR2A	chr4:87855365-87858037	PBDE	blood:	n/a	n/a
37	JUN	chr4:87857152-87857848	K562	blood:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857424-87857433
38	IRF1	chr4:87857018-87857831	K562	blood:	n/a	n/a
39	ELF1	chr4:87857611-87857982	HepG2	liver:	n/a	chr4:87857852-87857863 chr4:87857852-87857863
40	NR2F2	chr4:87857004-87857949	K562	blood:	n/a	n/a
41	EP300	chr4:87857117-87857829	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:87856806-87857815	HepG2	liver:	n/a	n/a
43	RUNX3	chr4:87855665-87857827	GM12878	blood:	n/a	n/a
44	MAX	chr4:87856892-87857881	Hela-S3	cervix:	n/a	n/a
45	RXRA	chr4:87857502-87857876	HepG2	liver:	n/a	n/a
46	RCOR1	chr4:87855301-87857823	K562	blood:	n/a	n/a
47	HDAC2	chr4:87856826-87857937	HepG2	liver:	n/a	chr4:87857728-87857742
48	BCLAF1	chr4:87857261-87857980	GM12878	blood:	n/a	n/a
49	MYC	chr4:87855259-87858147	K562	blood:	n/a	chr4:87856044-87856054 chr4:87856093-87856103
50	FOXA2	chr4:87857133-87857986	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
2	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
3	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
4	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000172493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10015508	1.00[CHB][hapmap]
rs10020861	1.00[CHB][hapmap]
rs13120839	1.00[CHB][hapmap]
rs13141697	1.00[CHB][hapmap]
rs17012114	1.00[CHB][hapmap]
rs17012130	1.00[CHB][hapmap]
rs17012152	1.00[AFR][1000 genomes]
rs17012191	1.00[AFR][1000 genomes]
rs17012211	1.00[AFR][1000 genomes]
rs17012218	1.00[AFR][1000 genomes]
rs6811350	1.00[CHB][hapmap]
rs727143	1.00[CHB][hapmap]
rs7690165	1.00[CHB][hapmap]
rs9654158	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87854800-87858600	Active TSS	Right Ventricle	heart
2	chr4:87854800-87859200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:87855000-87858000	Active TSS	Duodenum Mucosa	Duodenum
4	chr4:87855000-87858000	Active TSS	HMEC	breast
5	chr4:87855000-87858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:87855000-87858400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr4:87855000-87858400	Active TSS	Psoas Muscle	Psoas
8	chr4:87855000-87859000	Active TSS	Colonic Mucosa	Colon
9	chr4:87855000-87859000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr4:87855000-87859800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:87855200-87858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:87855200-87858200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:87855200-87858200	Active TSS	Brain Hippocampus Middle	brain
14	chr4:87855200-87858200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:87855200-87858200	Active TSS	A549	lung
16	chr4:87855200-87858400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:87855200-87858400	Active TSS	Placenta Amnion	Placenta Amnion
18	chr4:87855200-87858600	Active TSS	Stomach Mucosa	stomach
19	chr4:87855200-87859000	Active TSS	Fetal Intestine Large	intestine
20	chr4:87855200-87859200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr4:87855200-87859200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:87855200-87859800	Active TSS	GM12878-XiMat	blood
23	chr4:87855200-87859800	Active TSS	Hela-S3	cervix
24	chr4:87855400-87858000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:87855400-87858000	Active TSS	Rectal Smooth Muscle	rectum
26	chr4:87855400-87858200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr4:87855400-87858200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:87855400-87858400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:87855400-87858400	Active TSS	Fetal Kidney	kidney
30	chr4:87855400-87859000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:87855400-87859200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr4:87855400-87859800	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr4:87855400-87859800	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr4:87855600-87858000	Active TSS	Brain Cingulate Gyrus	brain
35	chr4:87855600-87858000	Active TSS	Brain Substantia Nigra	brain
36	chr4:87855600-87858200	Active TSS	Brain Anterior Caudate	brain
37	chr4:87855600-87858400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:87855600-87858400	Active TSS	NHEK	skin
39	chr4:87855600-87858600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:87855600-87858600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:87855600-87858800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:87856000-87858400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:87856200-87858600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:87856400-87858000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:87856600-87858200	Bivalent/Poised TSS	HepG2	liver
46	chr4:87856600-87858400	Active TSS	Right Atrium	heart
47	chr4:87856600-87861600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:87856800-87858000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr4:87856800-87858200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr4:87856800-87858200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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