Variant report

Variant	rs55676788
Chromosome Location	chr16:71560153-71560154
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	TEAD4	chr16:71560149-71560574	ECC-1	luminal epithelium:	n/a	n/a
2	YY1	chr16:71559874-71560756	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOS	chr16:71560144-71560485	MCF10A-Er-Src	breast:	n/a	chr16:71560322-71560330
4	POLR2A	chr16:71559929-71560763	NB4	blood:	n/a	n/a
5	POLR2A	chr16:71559927-71560520	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr16:71559997-71560569	H1-hESC	embryonic stem cell:	n/a	chr16:71560339-71560348
7	GABPA	chr16:71560001-71560473	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr16:71559821-71560635	H1-hESC	embryonic stem cell:	n/a	chr16:71559997-71560011 chr16:71560240-71560251
9	YY1	chr16:71559895-71560746	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr16:71559817-71560857	H1-hESC	embryonic stem cell:	n/a	n/a
11	HDAC2	chr16:71560057-71560310	H1-hESC	embryonic stem cell:	n/a	n/a
12	GTF2F1	chr16:71559973-71560514	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr16:71559894-71560838	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTBP2	chr16:71559913-71560780	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr16:71560027-71560561	H1-hESC	embryonic stem cell:	n/a	chr16:71560339-71560348
16	MXI1	chr16:71560036-71560485	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr16:71559899-71560738	NB4	blood:	n/a	chr16:71560339-71560348
18	CHD2	chr16:71559992-71560541	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr16:71559616-71561055	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOS	chr16:71560144-71560491	MCF10A-Er-Src	breast:	n/a	chr16:71560322-71560330
21	CEBPB	chr16:71560132-71560437	IMR90	lung:	n/a	n/a
22	MAZ	chr16:71560082-71560227	GM12878	blood:	n/a	n/a
23	TBP	chr16:71559996-71560705	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr16:71560054-71560619	U87	brain:	n/a	n/a
25	JUN	chr16:71560142-71560487	H1-hESC	embryonic stem cell:	n/a	chr16:71560322-71560330
26	SIN3A	chr16:71559942-71560812	H1-hESC	embryonic stem cell:	n/a	chr16:71560789-71560797
27	POLR2A	chr16:71560017-71560322	Gliobla	brain:	n/a	n/a
28	POLR2A	chr16:71560053-71560700	U87	brain:	n/a	n/a
29	TEAD4	chr16:71559960-71560596	H1-hESC	embryonic stem cell:	n/a	n/a
30	ATF2	chr16:71559924-71560608	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr16:71560085-71560552	HCT-116	colon:	n/a	n/a
32	POLR2A	chr16:71559835-71560803	H1-hESC	embryonic stem cell:	n/a	n/a
33	NANOG	chr16:71560121-71560529	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr16:71559885-71560655	H1-hESC	embryonic stem cell:	n/a	chr16:71560096-71560105 chr16:71560322-71560330
35	KAP1	chr16:71560008-71560793	HEK293	kidney:	n/a	chr16:71560320-71560329
36	MAX	chr16:71560107-71560547	SK-N-SH	brain:	n/a	chr16:71560339-71560348
37	POLR2A	chr16:71559884-71560653	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD1	chr16:71559756-71560734	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF7	chr16:71559865-71560646	H1-hESC	embryonic stem cell:	n/a	n/a
40	KAP1	chr16:71560053-71560945	U2OS	brain:	n/a	chr16:71560320-71560329
41	ZNF143	chr16:71560049-71560470	H1-hESC	embryonic stem cell:	n/a	n/a
42	JUND	chr16:71560073-71560423	H1-hESC	embryonic stem cell:	n/a	chr16:71560096-71560105 chr16:71560322-71560330
43	MAX	chr16:71559848-71561126	NB4	blood:	n/a	chr16:71560339-71560348
44	TAF1	chr16:71559806-71560833	H1-hESC	embryonic stem cell:	n/a	n/a
45	JUND	chr16:71559837-71560949	SK-N-SH	brain:	n/a	chr16:71560096-71560105 chr16:71560322-71560330
46	MAX	chr16:71559906-71560570	H1-hESC	embryonic stem cell:	n/a	chr16:71560339-71560348
47	MAX	chr16:71559892-71560608	H1-hESC	embryonic stem cell:	n/a	chr16:71560339-71560348
48	SP1	chr16:71559821-71560661	H1-hESC	embryonic stem cell:	n/a	chr16:71559997-71560011 chr16:71560240-71560251

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71547709..71549497-chr16:71558790..71560524,2	MCF-7	breast:

Variant related genes	Relation type
CHST4	TF binding region
ENSG00000260520	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3794689	1.00[AFR][1000 genomes]
rs4149497	0.90[EUR][1000 genomes]
rs67700822	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv906892	chr16:71526720-71570413	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71556000-71563200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:71558400-71560800	Enhancers	HSMM	muscle
3	chr16:71558400-71561000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr16:71558800-71560200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr16:71558800-71560600	Flanking Active TSS	HMEC	breast
6	chr16:71559000-71560200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr16:71559000-71560200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr16:71559000-71560200	Enhancers	NHEK	skin
9	chr16:71559000-71560400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:71559000-71560600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr16:71559000-71560800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:71559200-71560200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:71559200-71560400	Enhancers	Ovary	ovary
14	chr16:71559200-71560800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr16:71559400-71560800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:71559400-71560800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:71559600-71560600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:71559600-71561000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr16:71559600-71561200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr16:71559800-71560200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr16:71559800-71560400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr16:71559800-71560600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
23	chr16:71559800-71560800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr16:71560000-71560200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr16:71560000-71560200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:71560000-71560200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr16:71560000-71560200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
28	chr16:71560000-71560200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:71560000-71560200	Bivalent Enhancer	Left Ventricle	heart
30	chr16:71560000-71560200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr16:71560000-71560200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr16:71560000-71560200	Flanking Active TSS	HSMMtube	muscle
33	chr16:71560000-71560200	Flanking Bivalent TSS/Enh	Osteobl	bone
34	chr16:71560000-71560400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr16:71560000-71560400	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr16:71560000-71560400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr16:71560000-71560400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr16:71560000-71560400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr16:71560000-71560400	Enhancers	Esophagus	oesophagus
40	chr16:71560000-71560400	Flanking Active TSS	GM12878-XiMat	blood
41	chr16:71560000-71560400	Enhancers	NHDF-Ad	bronchial
42	chr16:71560000-71560600	Active TSS	H1 Cell Line	embryonic stem cell
43	chr16:71560000-71560600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr16:71560000-71560600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:71560000-71560600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr16:71560000-71560600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:71560000-71560600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr16:71560000-71560600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:71560000-71560600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:71560000-71560600	Bivalent Enhancer	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links