Variant report

Variant	rs28688431
Chromosome Location	chr18:28623001-28623002
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	MAX	chr18:28622079-28623294	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr18:28622960-28623110	NHEK	skin:	n/a	n/a
3	MAX	chr18:28622310-28623339	A549	lung:	n/a	n/a
4	MYC	chr18:28622948-28623327	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr18:28623000-28623150	HMEC	breast:	n/a	n/a
6	RAD21	chr18:28622906-28623316	H1-hESC	embryonic stem cell:	n/a	n/a
7	NANOG	chr18:28622880-28623162	H1-hESC	embryonic stem cell:	n/a	chr18:28623065-28623074
8	POLR2A	chr18:28622489-28623124	A549	lung:	n/a	n/a
9	STAT3	chr18:28622751-28623007	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr18:28622782-28623040	A549	lung:	n/a	n/a
11	MYC	chr18:28622124-28623203	MCF10A-Er-Src	breast:	n/a	n/a
12	KAP1	chr18:28620799-28623433	HEK293	kidney:	n/a	n/a
13	JUND	chr18:28622636-28623147	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr18:28622999-28623144	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr18:28622630-28623035	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr18:28622598-28623101	MCF10A-Er-Src	breast:	n/a	chr18:28622853-28622862
17	STAT3	chr18:28622741-28623250	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr18:28621804-28623302	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF263	chr18:28620841-28623317	HEK293-T-REx	kidney:	n/a	n/a
20	MAX	chr18:28622126-28623242	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr18:28619436-28623145	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr18:28618905-28623310	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr18:28622750-28623203	ECC-1	luminal epithelium:	n/a	n/a
24	KAP1	chr18:28622128-28623198	U2OS	brain:	n/a	n/a
25	CTCF	chr18:28623000-28623150	HepG2	liver:	n/a	n/a
26	TBP	chr18:28622971-28623172	H1-hESC	embryonic stem cell:	n/a	n/a
27	STAT3	chr18:28622765-28623329	MCF10A-Er-Src	breast:	n/a	chr18:28623270-28623278
28	SIN3A	chr18:28622260-28623159	H1-hESC	embryonic stem cell:	n/a	chr18:28622867-28622880
29	POLR2A	chr18:28622203-28623136	HEK293	kidney:	n/a	n/a
30	STAT3	chr18:28622721-28623245	MCF10A-Er-Src	breast:	n/a	n/a
31	TAF1	chr18:28622110-28623232	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr18:28620912-28623325	H1-hESC	embryonic stem cell:	n/a	chr18:28621645-28621654 chr18:28621932-28621939 chr18:28621326-28621340 chr18:28621932-28621939 chr18:28622853-28622862 chr18:28622195-28622202 chr18:28621931-28621943 chr18:28621932-28621939
33	SUZ12	chr18:28620850-28623202	NT2-D1	testis:	n/a	n/a
34	TCF7L2	chr18:28622250-28623026	HCT-116	colon:	n/a	n/a
35	CTBP2	chr18:28620948-28623230	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr18:28622940-28623090	HMEC	breast:	n/a	n/a
37	YY1	chr18:28622409-28623098	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28622482..28623001-chrX:152864333..152864870,2	MCF-7	breast:

Variant related genes	Relation type
DSC3	TF binding region
ENSG00000260081	Chromatin interaction
ENSG00000147382	Chromatin interaction

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

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

rs_ID	r²[population]
rs12456806	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12458126	0.89[ASN][1000 genomes]
rs1586958	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1586959	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1586960	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1586961	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17726372	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1816635	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28414229	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28657717	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41465650	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4799562	0.83[ASN][1000 genomes]
rs7235088	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8086281	1.00[EUR][1000 genomes]

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	nsv833613	chr18:28446454-28623599	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv961134	chr18:28612225-28625943	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28619400-28623200	Active TSS	Placenta Amnion	Placenta Amnion
2	chr18:28619800-28623200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:28620400-28623400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr18:28620600-28623800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr18:28620800-28623200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:28621000-28623200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:28621000-28623200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr18:28621000-28623200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr18:28621000-28623400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr18:28621200-28623200	Active TSS	Esophagus	oesophagus
11	chr18:28621200-28623200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
12	chr18:28621400-28623200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:28621400-28623200	Flanking Bivalent TSS/Enh	Right Ventricle	heart
14	chr18:28621400-28623200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
15	chr18:28621400-28623200	Bivalent/Poised TSS	Thymus	Thymus
16	chr18:28621400-28623600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr18:28621600-28623200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr18:28621600-28623200	Bivalent/Poised TSS	NH-A	brain
19	chr18:28621600-28623400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr18:28621800-28623200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr18:28622000-28623200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr18:28622200-28623200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:28622200-28623200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr18:28622200-28623400	Active TSS	A549	lung
25	chr18:28622400-28623200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:28622400-28623200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:28622400-28623200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr18:28622400-28623200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
29	chr18:28622400-28623400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr18:28622600-28623200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
31	chr18:28622600-28623200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr18:28622600-28623200	Bivalent/Poised TSS	Colonic Mucosa	Colon
33	chr18:28622800-28623200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr18:28622800-28623200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
35	chr18:28622800-28623200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr18:28622800-28623200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
37	chr18:28622800-28623200	Enhancers	Gastric	stomach
38	chr18:28622800-28623200	Bivalent Enhancer	Stomach Mucosa	stomach
39	chr18:28622800-28623400	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr18:28623000-28623200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:28623000-28623200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr18:28623000-28623200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:28623000-28623200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr18:28623000-28623200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr18:28623000-28623200	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
46	chr18:28623000-28623200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr18:28623000-28623200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
48	chr18:28623000-28623200	Flanking Bivalent TSS/Enh	Liver	Liver
49	chr18:28623000-28623200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
50	chr18:28623000-28623200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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