Variant report

Variant	rs8099288
Chromosome Location	chr18:12465481-12465482
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12463744..12466333-chr18:12470245..12472659,2	K562	blood:
2	chr18:12464094..12466231-chr18:12487109..12489946,2	MCF-7	breast:
3	chr18:12464199..12466498-chr18:12531835..12534724,2	K562	blood:

Variant related genes	Relation type
ENSG00000238309	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12455439	0.84[EUR][1000 genomes]
rs12455481	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457760	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12608270	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958049	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12964631	0.86[EUR][1000 genomes]
rs17615158	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016707	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116004	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36109961	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58193967	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59992891	0.86[EUR][1000 genomes]
rs7234589	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234742	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8099288	RP11-861E21.2	cis	Thyroid	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
3	chr18:12439400-12468200	Weak transcription	K562	blood
4	chr18:12444000-12467400	Weak transcription	A549	lung
5	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12446200-12479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr18:12449600-12470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:12449600-12477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:12449800-12466800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr18:12449800-12470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:12449800-12477600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr18:12449800-12477600	Weak transcription	Spleen	Spleen
14	chr18:12449800-12477800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr18:12449800-12478000	Weak transcription	Gastric	stomach
16	chr18:12449800-12478000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr18:12449800-12479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr18:12450000-12478200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:12453400-12484400	Weak transcription	Hela-S3	cervix
20	chr18:12456800-12477400	Weak transcription	Fetal Kidney	kidney
21	chr18:12457800-12470400	Weak transcription	Fetal Brain Male	brain
22	chr18:12457800-12477600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr18:12458400-12465800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:12458600-12465800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr18:12458800-12465600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr18:12458800-12465600	Strong transcription	Adipose Nuclei	Adipose
27	chr18:12458800-12465800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr18:12458800-12466400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12459400-12465600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:12459600-12477600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:12459600-12478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr18:12460200-12478200	Weak transcription	NH-A	brain
33	chr18:12460200-12516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr18:12460400-12477600	Weak transcription	Lung	lung
35	chr18:12460400-12478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr18:12461000-12470200	Weak transcription	Brain Angular Gyrus	brain
37	chr18:12461200-12466000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr18:12461200-12470200	Weak transcription	NHEK	skin
39	chr18:12461200-12478200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr18:12461200-12481200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:12461400-12466000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:12461400-12477600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr18:12461400-12495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr18:12461600-12465800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:12461600-12470400	Weak transcription	HSMM	muscle
46	chr18:12461600-12477600	Weak transcription	Liver	Liver
47	chr18:12461800-12477600	Weak transcription	Colon Smooth Muscle	Colon
48	chr18:12461800-12478200	Weak transcription	HepG2	liver
49	chr18:12461800-12479800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr18:12462000-12466000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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