Variant report

Variant	rs12457086
Chromosome Location	chr18:39665475-39665476
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	POLR2A	chr18:39664721-39665559	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000267088	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10221315	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10468957	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775471	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11082257	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11659568	0.84[ASN][1000 genomes]
rs11660388	0.84[ASN][1000 genomes]
rs11660513	0.84[ASN][1000 genomes]
rs12326267	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327365	0.84[ASN][1000 genomes]
rs12455038	0.83[AMR][1000 genomes]
rs12455083	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12456084	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12456573	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12456761	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12456934	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12457082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457354	0.80[AMR][1000 genomes]
rs12457525	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12954202	0.83[ASN][1000 genomes]
rs12964834	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12964931	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12966303	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1432138	0.80[AMR][1000 genomes]
rs1557418	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1557419	0.84[ASN][1000 genomes]
rs1573497	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16975474	0.80[AMR][1000 genomes]
rs1941526	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1941532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1942151	0.80[AMR][1000 genomes]
rs1942152	0.80[AMR][1000 genomes]
rs1984366	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1984367	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2043220	0.80[AMR][1000 genomes]
rs2096896	0.84[ASN][1000 genomes]
rs2096897	0.84[ASN][1000 genomes]
rs2105680	0.84[ASN][1000 genomes]
rs2156015	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34966612	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3932738	0.84[ASN][1000 genomes]
rs3932739	0.84[ASN][1000 genomes]
rs4121647	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4121811	0.83[ASN][1000 genomes]
rs4890221	0.83[AMR][1000 genomes]
rs4890377	0.80[AMR][1000 genomes]
rs4890378	0.83[AMR][1000 genomes]
rs4890379	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5004531	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs536139	0.84[ASN][1000 genomes]
rs56147258	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs569983	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57794431	0.82[AMR][1000 genomes]
rs581950	0.81[EUR][1000 genomes]
rs60861018	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61107251	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62082282	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62082880	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62082911	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627099	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs639660	0.81[EUR][1000 genomes]
rs650586	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs667503	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66960332	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7237459	0.80[AMR][1000 genomes]
rs7504589	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8093251	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs948871	0.84[ASN][1000 genomes]
rs948872	0.83[ASN][1000 genomes]
rs948873	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9635942	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807114	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807400	0.80[AMR][1000 genomes]
rs9989595	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
4	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr18:39612200-39666400	Weak transcription	Gastric	stomach
6	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
7	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:39628600-39666200	Weak transcription	A549	lung
9	chr18:39634800-39674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:39644200-39674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr18:39648200-39666400	Weak transcription	Thymus	Thymus
12	chr18:39648200-39668200	Weak transcription	Brain Angular Gyrus	brain
13	chr18:39649200-39665600	Weak transcription	HepG2	liver
14	chr18:39649200-39674600	Weak transcription	Fetal Intestine Small	intestine
15	chr18:39653000-39666200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:39653000-39683400	Weak transcription	Aorta	Aorta
17	chr18:39653400-39665800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr18:39653400-39668000	Weak transcription	Pancreas	Pancrea
19	chr18:39653600-39669600	Weak transcription	NHLF	lung
20	chr18:39654000-39669600	Weak transcription	HSMMtube	muscle
21	chr18:39657600-39669600	Weak transcription	Lung	lung
22	chr18:39657800-39666200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr18:39657800-39666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr18:39657800-39668200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr18:39657800-39669000	Weak transcription	Fetal Brain Female	brain
26	chr18:39659000-39666400	Weak transcription	Hela-S3	cervix
27	chr18:39659000-39667600	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:39659000-39668800	Weak transcription	Fetal Kidney	kidney
29	chr18:39659400-39667200	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:39659600-39666400	Weak transcription	Fetal Muscle Leg	muscle
31	chr18:39659800-39668000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr18:39659800-39668200	Weak transcription	Brain Substantia Nigra	brain
33	chr18:39659800-39668600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr18:39659800-39669400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:39659800-39675400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:39660000-39666200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr18:39660000-39666400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr18:39660000-39674400	Weak transcription	Fetal Intestine Large	intestine
39	chr18:39660200-39666400	Weak transcription	Fetal Thymus	thymus
40	chr18:39660200-39668000	Weak transcription	Brain Anterior Caudate	brain
41	chr18:39660200-39670000	Weak transcription	Ovary	ovary
42	chr18:39660400-39668000	Weak transcription	Fetal Brain Male	brain
43	chr18:39660600-39666200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:39660800-39667200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr18:39660800-39669600	Weak transcription	Left Ventricle	heart
46	chr18:39661000-39666000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr18:39661200-39668200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr18:39661400-39666200	Weak transcription	Fetal Lung	lung
49	chr18:39661400-39666200	Weak transcription	NH-A	brain
50	chr18:39661800-39667600	Weak transcription	HMEC	breast

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