Variant report

Variant	rs530790
Chromosome Location	chr18:39663107-39663108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETBP1-8	chr18:39661838-39663348	NONHSAT059059

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1469617	0.83[AMR][1000 genomes]
rs472141	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs488202	1.00[AMR][1000 genomes]
rs500702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs508867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs530986	1.00[AMR][1000 genomes]
rs555275	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs569070	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs591823	0.90[AFR][1000 genomes]
rs631388	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs638646	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs650025	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs670596	0.89[AFR][1000 genomes]
rs685164	0.83[AFR][1000 genomes]
rs8085816	0.83[AMR][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
3	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
5	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:39612200-39666400	Weak transcription	Gastric	stomach
7	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
8	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:39620800-39664200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr18:39628600-39666200	Weak transcription	A549	lung
12	chr18:39634800-39674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr18:39639400-39664000	Weak transcription	K562	blood
14	chr18:39644200-39674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:39644600-39665000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr18:39644800-39664200	Strong transcription	Liver	Liver
17	chr18:39644800-39665000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr18:39645000-39664000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:39648200-39665400	Weak transcription	Spleen	Spleen
20	chr18:39648200-39666400	Weak transcription	Thymus	Thymus
21	chr18:39648200-39668200	Weak transcription	Brain Angular Gyrus	brain
22	chr18:39649200-39665600	Weak transcription	HepG2	liver
23	chr18:39649200-39674600	Weak transcription	Fetal Intestine Small	intestine
24	chr18:39649600-39664400	Strong transcription	HSMM	muscle
25	chr18:39650400-39665200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr18:39650600-39664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr18:39653000-39666200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr18:39653000-39683400	Weak transcription	Aorta	Aorta
29	chr18:39653200-39664000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr18:39653400-39665800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr18:39653400-39668000	Weak transcription	Pancreas	Pancrea
32	chr18:39653600-39669600	Weak transcription	NHLF	lung
33	chr18:39654000-39664000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr18:39654000-39669600	Weak transcription	HSMMtube	muscle
35	chr18:39655400-39663200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:39655800-39664200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr18:39655800-39665000	Strong transcription	GM12878-XiMat	blood
38	chr18:39656400-39663400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr18:39656400-39663400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr18:39656400-39663600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr18:39656400-39664000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr18:39656400-39664200	Strong transcription	Adipose Nuclei	Adipose
43	chr18:39656400-39664400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:39657000-39664200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr18:39657200-39664000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr18:39657600-39669600	Weak transcription	Lung	lung
47	chr18:39657800-39664400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr18:39657800-39666200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr18:39657800-39666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr18:39657800-39668200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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