Variant report

Variant	rs62085039
Chromosome Location	chr18:8341925-8341926
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	ATF3	chr18:8341465-8342254	A549	lung:	n/a	n/a
2	EP300	chr18:8341309-8342654	A549	lung:	n/a	chr18:8342167-8342180 chr18:8342057-8342071
3	GATA3	chr18:8341684-8342045	MCF-7	breast:	n/a	chr18:8342014-8342021
4	MAFK	chr18:8341715-8342124	IMR90	lung:	n/a	chr18:8342013-8342027 chr18:8342014-8342025
5	MAX	chr18:8341527-8342227	A549	lung:	n/a	n/a
6	NFIC	chr18:8341491-8342028	HepG2	liver:	n/a	n/a
7	RXRA	chr18:8341391-8342199	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341843-8341859
8	HNF4G	chr18:8341524-8341996	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
9	RAD21	chr18:8341476-8342156	IMR90	lung:	n/a	chr18:8341605-8341612
10	YY1	chr18:8341724-8342068	HepG2	liver:	n/a	chr18:8341930-8341938 chr18:8341919-8341941 chr18:8341931-8341941
11	FOXA2	chr18:8341266-8342501	A549	lung:	n/a	chr18:8341775-8341787
12	MAFK	chr18:8341724-8342310	HepG2	liver:	n/a	chr18:8342013-8342027 chr18:8342014-8342025
13	HNF4A	chr18:8341454-8342019	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
14	TEAD4	chr18:8341517-8342298	A549	lung:	n/a	n/a
15	PBX3	chr18:8341419-8342248	A549	lung:	n/a	n/a
16	ZBTB33	chr18:8341456-8342204	A549	lung:	n/a	n/a
17	USF1	chr18:8341495-8342768	A549	lung:	n/a	n/a
18	MAX	chr18:8341311-8342447	A549	lung:	n/a	n/a
19	NR3C1	chr18:8341411-8342297	A549	lung:	n/a	chr18:8342103-8342116
20	HDAC2	chr18:8341490-8342208	HepG2	liver:	n/a	n/a
21	MXI1	chr18:8341480-8342319	HepG2	liver:	n/a	n/a
22	HNF4A	chr18:8341602-8341963	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
23	JUN	chr18:8341562-8342023	HepG2	liver:	n/a	chr18:8341681-8341690 chr18:8341680-8341689
24	MAFF	chr18:8341654-8342320	HepG2	liver:	n/a	n/a
25	TEAD4	chr18:8341365-8342310	A549	lung:	n/a	n/a
26	FOSL2	chr18:8341370-8341988	HepG2	liver:	n/a	chr18:8341459-8341470 chr18:8341681-8341690 chr18:8341680-8341689
27	JUND	chr18:8341403-8342332	A549	lung:	n/a	chr18:8341459-8341470 chr18:8341681-8341690 chr18:8341680-8341689
28	MAX	chr18:8341217-8342467	A549	lung:	n/a	n/a
29	MYBL2	chr18:8341474-8342110	HepG2	liver:	n/a	n/a
30	PBX3	chr18:8341525-8342212	A549	lung:	n/a	n/a
31	RAD21	chr18:8341541-8342082	A549	lung:	n/a	chr18:8341605-8341612
32	NFIC	chr18:8341407-8342090	HepG2	liver:	n/a	n/a
33	SIX5	chr18:8341615-8341962	A549	lung:	n/a	chr18:8341809-8341818
34	YY1	chr18:8341422-8342202	A549	lung:	n/a	chr18:8341930-8341938 chr18:8341919-8341941 chr18:8341931-8341941
35	SIN3AK20	chr18:8341499-8341961	A549	lung:	n/a	n/a
36	MBD4	chr18:8341530-8342038	HepG2	liver:	n/a	n/a
37	EP300	chr18:8341479-8342151	HepG2	liver:	n/a	chr18:8342057-8342071
38	CEBPB	chr18:8341487-8342380	A549	lung:	n/a	n/a
39	NR3C1	chr18:8341374-8342287	A549	lung:	n/a	chr18:8342103-8342116
40	CREB1	chr18:8341418-8342282	A549	lung:	n/a	n/a
41	MAFK	chr18:8341570-8342341	HepG2	liver:	n/a	chr18:8342013-8342027 chr18:8342014-8342025
42	TCF12	chr18:8341489-8342222	A549	lung:	n/a	n/a
43	MAX	chr18:8341530-8341967	HepG2	liver:	n/a	n/a
44	RCOR1	chr18:8341601-8342203	HepG2	liver:	n/a	n/a
45	CEBPB	chr18:8341515-8342321	HepG2	liver:	n/a	n/a
46	JUND	chr18:8341482-8342066	HepG2	liver:	n/a	chr18:8341681-8341690 chr18:8341680-8341689
47	MYBL2	chr18:8341479-8342139	HepG2	liver:	n/a	n/a
48	EP300	chr18:8341452-8342189	HepG2	liver:	n/a	chr18:8342167-8342180 chr18:8342057-8342071
49	CREB1	chr18:8341354-8342063	A549	lung:	n/a	n/a
50	CEBPB	chr18:8341556-8342240	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:8336321..8338584-chr18:8341680..8343766,3	K562	blood:

Variant related genes	Relation type
ENSG00000268046	TF binding region
ENSG00000268046	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16953299	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16953309	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16953319	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16953329	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16953340	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16953349	0.95[EUR][1000 genomes]
rs2446503	0.85[EUR][1000 genomes]
rs2509546	0.92[EUR][1000 genomes]
rs592535	0.85[EUR][1000 genomes]
rs59726215	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs598149	0.85[EUR][1000 genomes]
rs603476	0.85[EUR][1000 genomes]
rs603810	0.89[EUR][1000 genomes]
rs606954	0.85[EUR][1000 genomes]
rs611709	0.89[EUR][1000 genomes]
rs613113	0.89[EUR][1000 genomes]
rs62085040	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62085041	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62085047	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62085048	0.95[EUR][1000 genomes]
rs62089873	0.81[EUR][1000 genomes]
rs62089899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635416	0.81[EUR][1000 genomes]
rs656568	0.81[EUR][1000 genomes]
rs665525	0.85[EUR][1000 genomes]
rs685266	0.85[EUR][1000 genomes]
rs694406	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057288	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv543639	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3351324	chr18:8250514-8405140	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1058445	chr18:8270681-8421249	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8320800-8357200	Weak transcription	Thymus	Thymus
2	chr18:8328000-8342600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr18:8329600-8358200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:8329800-8365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:8339400-8342000	Enhancers	Right Atrium	heart
6	chr18:8339400-8342200	Enhancers	Left Ventricle	heart
7	chr18:8339400-8342200	Enhancers	Right Ventricle	heart
8	chr18:8339400-8342600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr18:8339400-8344200	Enhancers	Fetal Heart	heart
10	chr18:8339600-8342200	Enhancers	Pancreas	Pancrea
11	chr18:8339600-8344000	Enhancers	Fetal Lung	lung
12	chr18:8340200-8344200	Weak transcription	Brain Anterior Caudate	brain
13	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
14	chr18:8340400-8342200	Enhancers	Aorta	Aorta
15	chr18:8340800-8343000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr18:8340800-8344200	Enhancers	Stomach Mucosa	stomach
17	chr18:8341000-8342000	Enhancers	HSMMtube	muscle
18	chr18:8341000-8342200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:8341000-8343000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:8341000-8343000	Enhancers	Liver	Liver
21	chr18:8341200-8342400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr18:8341200-8342600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:8341200-8342600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr18:8341200-8342600	Enhancers	NH-A	brain
25	chr18:8341200-8342600	Enhancers	Osteobl	bone
26	chr18:8341200-8343800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr18:8341400-8342000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr18:8341400-8342000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:8341400-8342000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr18:8341400-8342000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr18:8341400-8342000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr18:8341400-8342000	Enhancers	Fetal Muscle Trunk	muscle
33	chr18:8341400-8342000	Enhancers	Ovary	ovary
34	chr18:8341400-8342000	Enhancers	Stomach Smooth Muscle	stomach
35	chr18:8341400-8342200	Enhancers	Fetal Intestine Small	intestine
36	chr18:8341400-8342200	Enhancers	Fetal Stomach	stomach
37	chr18:8341400-8342200	Enhancers	Gastric	stomach
38	chr18:8341400-8342200	Enhancers	Lung	lung
39	chr18:8341400-8342200	Flanking Active TSS	HepG2	liver
40	chr18:8341400-8342400	Enhancers	NHDF-Ad	bronchial
41	chr18:8341400-8342400	Enhancers	NHLF	lung
42	chr18:8341400-8342600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:8341400-8342800	Enhancers	Fetal Kidney	kidney
44	chr18:8341400-8343600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr18:8341600-8342000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr18:8341600-8342000	Enhancers	Fetal Intestine Large	intestine
47	chr18:8341600-8342200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr18:8341600-8342200	Enhancers	Adipose Nuclei	Adipose
49	chr18:8341600-8342200	Weak transcription	Brain Hippocampus Middle	brain
50	chr18:8341600-8342200	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links