Variant report

Variant	rs504302
Chromosome Location	chr18:39662517-39662518
allele	A/G
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: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1790376	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474605	0.85[CEU][hapmap]
rs620052	0.95[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs504302	PIK3C3	cis	parietal	SCAN

Chromatin state (count:111 , 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	chr18:39644800-39662800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr18:39644800-39664200	Strong transcription	Liver	Liver
18	chr18:39644800-39665000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr18:39645000-39664000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr18:39648200-39665400	Weak transcription	Spleen	Spleen
21	chr18:39648200-39666400	Weak transcription	Thymus	Thymus
22	chr18:39648200-39668200	Weak transcription	Brain Angular Gyrus	brain
23	chr18:39649200-39665600	Weak transcription	HepG2	liver
24	chr18:39649200-39674600	Weak transcription	Fetal Intestine Small	intestine
25	chr18:39649600-39664400	Strong transcription	HSMM	muscle
26	chr18:39650000-39662600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr18:39650400-39665200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr18:39650600-39664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr18:39652200-39662800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr18:39653000-39666200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:39653000-39683400	Weak transcription	Aorta	Aorta
32	chr18:39653200-39664000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr18:39653400-39665800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:39653400-39668000	Weak transcription	Pancreas	Pancrea
35	chr18:39653600-39669600	Weak transcription	NHLF	lung
36	chr18:39654000-39662800	Weak transcription	NHDF-Ad	bronchial
37	chr18:39654000-39664000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr18:39654000-39669600	Weak transcription	HSMMtube	muscle
39	chr18:39655400-39663200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:39655800-39662800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr18:39655800-39664200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr18:39655800-39665000	Strong transcription	GM12878-XiMat	blood
43	chr18:39656400-39663400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr18:39656400-39663400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr18:39656400-39663600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr18:39656400-39664000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr18:39656400-39664200	Strong transcription	Adipose Nuclei	Adipose
48	chr18:39656400-39664400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr18:39656600-39662600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr18:39657000-39664200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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