Variant report

Variant	rs1792658
Chromosome Location	chr18:45382605-45382606
allele	A/C
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	POLR2A	chr18:45381273-45383044	A549	lung:	n/a	n/a
2	POLR2A	chr18:45382152-45383089	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr18:45381207-45383097	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000267541	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10502890	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs11082641	0.83[YRI][hapmap]
rs12457664	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs12458238	0.83[YRI][hapmap]
rs12968493	0.83[LWK][hapmap]
rs12969725	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs1539871	0.89[LWK][hapmap];0.87[YRI][hapmap]
rs1573362	0.83[YRI][hapmap]
rs1787186	0.81[LWK][hapmap]
rs1787196	0.81[AFR][1000 genomes]
rs1787199	0.87[YRI][hapmap]
rs1792666	0.87[YRI][hapmap]
rs1792668	0.84[LWK][hapmap];0.91[YRI][hapmap]
rs1792674	0.84[LWK][hapmap];0.87[YRI][hapmap]
rs1792684	0.81[LWK][hapmap];0.87[YRI][hapmap]
rs1792686	0.89[LWK][hapmap];0.87[YRI][hapmap]
rs1792687	0.81[LWK][hapmap];0.87[YRI][hapmap]
rs1792689	0.83[YRI][hapmap]
rs1942158	0.83[YRI][hapmap]
rs2012555	0.84[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs948602	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057722	chr18:45343965-45401360	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1058673	chr18:45360012-45404492	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1059186	chr18:45360012-45407405	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1062894	chr18:45368587-45387738	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1066394	chr18:45368587-45394386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1060581	chr18:45368587-45397623	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv1057525	chr18:45368587-45407405	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv1064282	chr18:45369857-45404768	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1064797	chr18:45372027-45394386	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1063859	chr18:45372027-45404492	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1062318	chr18:45374239-45394780	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1055814	chr18:45374239-45395377	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1057298	chr18:45374239-45404428	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1062731	chr18:45374239-45404768	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1058128	chr18:45374658-45394780	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1065607	chr18:45374658-45404751	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1792658	PPOX	trans	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
4	chr18:45366200-45390000	Weak transcription	Colonic Mucosa	Colon
5	chr18:45366400-45384000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr18:45366400-45384000	Weak transcription	Brain Angular Gyrus	brain
7	chr18:45366400-45384000	Weak transcription	Esophagus	oesophagus
8	chr18:45366600-45408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:45368200-45384000	Weak transcription	Stomach Mucosa	stomach
10	chr18:45369800-45383600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr18:45369800-45384000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:45369800-45384000	Weak transcription	Fetal Stomach	stomach
13	chr18:45369800-45386400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:45372000-45384000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:45372200-45386200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:45372200-45396000	Weak transcription	NHLF	lung
17	chr18:45373200-45384000	Weak transcription	Gastric	stomach
18	chr18:45373200-45384000	Weak transcription	Pancreas	Pancrea
19	chr18:45375200-45384200	Weak transcription	K562	blood
20	chr18:45375400-45384000	Weak transcription	NH-A	brain
21	chr18:45375600-45383400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr18:45375600-45384000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr18:45375600-45384000	Weak transcription	Osteobl	bone
24	chr18:45375800-45383600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr18:45375800-45384000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr18:45375800-45384000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr18:45375800-45384000	Weak transcription	HepG2	liver
28	chr18:45380000-45384000	Strong transcription	A549	lung
29	chr18:45380200-45383000	Weak transcription	Hela-S3	cervix
30	chr18:45380600-45384000	Weak transcription	NHEK	skin
31	chr18:45380600-45386800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:45380800-45383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:45380800-45384000	Weak transcription	HMEC	breast
34	chr18:45381000-45383000	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr18:45381200-45382800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr18:45381200-45383000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:45381200-45383000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr18:45381200-45383000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
39	chr18:45381200-45383000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr18:45381200-45383000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr18:45381200-45383000	ZNF genes & repeats	Liver	Liver
42	chr18:45381200-45383000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr18:45381200-45383000	ZNF genes & repeats	Fetal Kidney	kidney
44	chr18:45381200-45383000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
45	chr18:45381200-45383400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr18:45381200-45386800	ZNF genes & repeats	Fetal Lung	lung
47	chr18:45381200-45387000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr18:45381400-45383200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr18:45381400-45383200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
50	chr18:45381400-45384000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links