Variant report

Variant	rs329016
Chromosome Location	chr18:9503124-9503125
allele	G/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	SETDB1	chr18:9502869-9503234	K562	blood:	n/a	n/a
2	TRIM28	chr18:9502935-9503154	K562	blood:	n/a	n/a
3	CBX3	chr18:9502815-9503270	K562	blood:	n/a	n/a
4	RXRA	chr18:9503001-9503413	HepG2	liver:	n/a	n/a
5	KAP1	chr18:9502831-9503139	K562	blood:	n/a	n/a
6	SETDB1	chr18:9502796-9503434	U2OS	brain:	n/a	n/a
7	CBX3	chr18:9502868-9503215	K562	blood:	n/a	n/a
8	POU2F2	chr18:9502975-9503147	GM12878	blood:	n/a	n/a
9	POLR2A	chr18:9503087-9503261	Gliobla	brain:	n/a	n/a
10	TRIM28	chr18:9502847-9503271	K562	blood:	n/a	n/a
11	SP1	chr18:9503116-9503425	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9475513..9478380-chr18:9502080..9503975,2	K562	blood:

Variant related genes	Relation type
ENSG00000266805	TF binding region
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1049553	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11081480	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs167897	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120318	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs384178	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs389066	0.85[EUR][1000 genomes]
rs449932	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57315808	0.83[EUR][1000 genomes]
rs59365153	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60376740	0.83[EUR][1000 genomes]
rs6506672	0.83[EUR][1000 genomes]
rs6506673	0.85[EUR][1000 genomes]
rs7232950	0.85[EUR][1000 genomes]
rs7233044	0.85[EUR][1000 genomes]
rs7242756	0.80[EUR][1000 genomes]
rs72936444	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9477000-9514000	Weak transcription	NH-A	brain
2	chr18:9477200-9513800	Weak transcription	HSMM	muscle
3	chr18:9477800-9503200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr18:9478000-9503400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr18:9478000-9508400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr18:9478000-9522400	Weak transcription	Hela-S3	cervix
7	chr18:9479000-9514000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:9479000-9533200	Weak transcription	Aorta	Aorta
9	chr18:9479000-9533600	Weak transcription	Gastric	stomach
10	chr18:9480200-9513800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr18:9483000-9513800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:9492600-9514000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:9492800-9503400	Weak transcription	A549	lung
14	chr18:9493800-9506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:9495000-9506000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr18:9495000-9507600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr18:9495000-9518000	Weak transcription	Liver	Liver
18	chr18:9495000-9518000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr18:9495200-9504600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:9495200-9506200	Weak transcription	Left Ventricle	heart
21	chr18:9495200-9506200	Weak transcription	Psoas Muscle	Psoas
22	chr18:9495200-9508200	Weak transcription	Ovary	ovary
23	chr18:9495200-9530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr18:9495200-9533600	Weak transcription	Right Ventricle	heart
25	chr18:9495400-9512800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr18:9495400-9514000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr18:9495400-9524000	Weak transcription	Spleen	Spleen
28	chr18:9495400-9534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr18:9495800-9514000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr18:9495800-9517000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr18:9496000-9513800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:9496200-9507200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr18:9496600-9505000	Weak transcription	Stomach Mucosa	stomach
34	chr18:9496800-9506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:9496800-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:9497000-9506000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:9497400-9532600	Weak transcription	Colonic Mucosa	Colon
38	chr18:9497600-9517200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:9497800-9513800	Weak transcription	NHEK	skin
40	chr18:9498400-9523200	Weak transcription	Esophagus	oesophagus
41	chr18:9499400-9503600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:9499400-9525000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr18:9500400-9506400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:9500600-9506200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr18:9500800-9503800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr18:9500800-9504000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr18:9500800-9535000	Weak transcription	Fetal Heart	heart
48	chr18:9501200-9503600	Weak transcription	HepG2	liver
49	chr18:9501600-9504800	Weak transcription	K562	blood
50	chr18:9502000-9514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links