Variant report

Variant	rs4788562
Chromosome Location	chr16:71879298-71879299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr16:71878934-71880136	GM12878	blood:	n/a	n/a
2	PML	chr16:71878906-71880606	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:71879296-71880870	GM12878	blood:	n/a	n/a
4	JUN	chr16:71879284-71880152	K562	blood:	n/a	chr16:71880005-71880013
5	POLR2A	chr16:71879091-71880794	HepG2	liver:	n/a	n/a
6	MXI1	chr16:71879185-71881058	SK-N-SH	brain:	n/a	chr16:71879714-71879723
7	POLR2A	chr16:71879235-71880287	GM12892	blood:	n/a	n/a
8	SIN3AK20	chr16:71879265-71880836	MCF-7	breast:	n/a	n/a
9	GATA1	chr16:71879127-71880046	PBDE	blood:	n/a	n/a
10	POLR2A	chr16:71879223-71880840	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr16:71879109-71880746	GM19193	blood:	n/a	n/a
12	MAZ	chr16:71879279-71880615	IMR90	lung:	n/a	n/a
13	POLR2A	chr16:71879198-71880721	GM18505	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71841032..71844957-chr16:71878188..71881982,18	MCF-7	breast:
2	chr16:71878397..71880298-chr16:71917810..71919339,2	MCF-7	breast:
3	chr16:71840441..71845295-chr16:71875076..71881716,14	K562	blood:
4	chr16:71756009..71758513-chr16:71878989..71881221,2	K562	blood:
5	chr16:71878736..71881297-chr20:57268088..57270906,2	MCF-7	breast:
6	chr16:71878320..71880402-chr16:71929242..71933378,4	MCF-7	breast:
7	chr16:71878006..71880307-chr16:74330687..74332965,2	MCF-7	breast:
8	chr16:71841284..71844520-chr16:71878157..71881366,4	K562	blood:
9	chr16:71874199..71877038-chr16:71877989..71879854,2	MCF-7	breast:
10	chr16:71879026..71881212-chr16:71914841..71917763,3	MCF-7	breast:
11	chr16:71832833..71836832-chr16:71876405..71879704,4	K562	blood:
12	chr16:71878378..71882676-chr16:71918678..71922110,3	K562	blood:
13	chr16:71755537..71758357-chr16:71878950..71881033,2	K562	blood:
14	chr16:71841846..71843774-chr16:71878337..71881293,3	MCF-7	breast:

No data

Variant related genes	Relation type
IST1	TF binding region
ATXN1L	TF binding region
ENSG00000040199	Chromatin interaction
ENSG00000261513	Chromatin interaction
ENSG00000103035	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000215440	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000261765	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11075908	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11649672	0.85[EUR][1000 genomes]
rs12102548	0.85[EUR][1000 genomes]
rs12444829	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12447045	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12449139	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12599192	0.83[EUR][1000 genomes]
rs12921084	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12926041	0.83[EUR][1000 genomes]
rs12926300	0.83[EUR][1000 genomes]
rs13329779	0.88[EUR][1000 genomes]
rs1834034	0.89[EUR][1000 genomes]
rs1834035	0.85[EUR][1000 genomes]
rs1981874	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2018384	0.85[EUR][1000 genomes]
rs2288029	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288031	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2335709	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2335710	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2335711	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2335712	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2335713	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2335714	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2335715	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28697038	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794692	0.86[EUR][1000 genomes]
rs4788446	0.80[EUR][1000 genomes]
rs4788447	0.93[EUR][1000 genomes]
rs4788449	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4788563	0.86[EUR][1000 genomes]
rs4788564	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4788566	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4788570	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788571	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788573	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788576	0.88[EUR][1000 genomes]
rs4788581	0.86[EUR][1000 genomes]
rs4788582	0.81[EUR][1000 genomes]
rs6499542	0.82[EUR][1000 genomes]
rs6499545	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6499551	0.88[EUR][1000 genomes]
rs6499552	0.88[EUR][1000 genomes]
rs7184437	0.93[EUR][1000 genomes]
rs7184486	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7187129	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7193731	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7205154	0.92[EUR][1000 genomes]
rs8044342	0.94[EUR][1000 genomes]
rs8046859	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8050488	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8050651	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8051038	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8057124	0.86[EUR][1000 genomes]
rs8058118	0.86[EUR][1000 genomes]
rs8059053	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8062946	0.88[EUR][1000 genomes]
rs8063324	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8063403	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9302631	0.88[EUR][1000 genomes]
rs9302632	0.87[EUR][1000 genomes]
rs9806882	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9806905	0.80[EUR][1000 genomes]
rs9932922	0.85[EUR][1000 genomes]
rs9934803	0.81[EUR][1000 genomes]
rs9934812	0.81[EUR][1000 genomes]
rs9937936	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 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	chr16:71876000-71879400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:71877000-71879400	Weak transcription	Fetal Heart	heart
3	chr16:71878400-71879400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:71878800-71880400	Active TSS	Colon Smooth Muscle	Colon
5	chr16:71879000-71879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:71879000-71879400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:71879000-71879400	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr16:71879000-71879400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:71879000-71879400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr16:71879000-71879400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr16:71879000-71879400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr16:71879000-71879400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr16:71879000-71879400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr16:71879000-71879400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr16:71879000-71879400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:71879000-71879400	Enhancers	Small Intestine	intestine
17	chr16:71879000-71879400	Enhancers	Stomach Mucosa	stomach
18	chr16:71879000-71879400	Active TSS	Stomach Smooth Muscle	stomach
19	chr16:71879000-71879400	Enhancers	Spleen	Spleen
20	chr16:71879000-71879400	Flanking Active TSS	GM12878-XiMat	blood
21	chr16:71879000-71879400	Flanking Active TSS	HepG2	liver
22	chr16:71879000-71879400	Enhancers	NH-A	brain
23	chr16:71879000-71879600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr16:71879000-71879600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:71879000-71879600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:71879000-71879600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:71879000-71879600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:71879000-71879600	Flanking Active TSS	Dnd41	blood
29	chr16:71879000-71880000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr16:71879000-71880200	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr16:71879000-71880200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr16:71879000-71880400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:71879000-71880400	Active TSS	Adipose Nuclei	Adipose
34	chr16:71879000-71880400	Active TSS	Colonic Mucosa	Colon
35	chr16:71879000-71880400	Active TSS	Duodenum Mucosa	Duodenum
36	chr16:71879000-71880400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr16:71879000-71880400	Active TSS	Rectal Smooth Muscle	rectum
38	chr16:71879000-71880600	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr16:71879000-71880600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr16:71879000-71880600	Active TSS	Brain Substantia Nigra	brain
41	chr16:71879000-71880800	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr16:71879000-71880800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr16:71879000-71880800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr16:71879000-71880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:71879000-71880800	Active TSS	Aorta	Aorta
46	chr16:71879000-71880800	Active TSS	A549	lung
47	chr16:71879000-71880800	Active TSS	HSMM	muscle
48	chr16:71879000-71880800	Active TSS	NHDF-Ad	bronchial
49	chr16:71879000-71881000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr16:71879000-71881000	Active TSS	H1 Cell Line	embryonic stem cell

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