Variant report

Variant	rs454768
Chromosome Location	chr18:29628863-29628864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29628181..29630533-chr18:29631429..29634258,2	K562	blood:
2	chr18:29627167..29630199-chr18:29636051..29638994,4	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10438934	0.90[ASN][1000 genomes]
rs11661718	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs170861	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17718949	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs189209	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2006768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432699	0.83[EUR][1000 genomes]
rs2433379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28621808	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911636	0.95[ASN][1000 genomes]
rs2912538	0.94[ASN][1000 genomes]
rs336272	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs336279	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs336280	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs336281	0.89[CEU][hapmap]
rs35672529	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs373667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799627	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641777	0.80[ASN][1000 genomes]
rs685446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs686271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7226543	0.89[JPT][hapmap]
rs72934872	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73413971	0.89[ASN][1000 genomes]
rs8086733	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
2	nsv1061305	chr18:29609935-29664528	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs454768	KIAA1012	cis	cerebellum	SCAN
rs454768	RP11-53I6.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29599600-29629600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:29600800-29632400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr18:29602600-29664200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr18:29604600-29656000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:29606800-29637000	Weak transcription	Brain Anterior Caudate	brain
6	chr18:29611800-29629000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr18:29615200-29648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr18:29616000-29640200	Weak transcription	Esophagus	oesophagus
9	chr18:29617200-29629600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr18:29618000-29629000	Weak transcription	Lung	lung
11	chr18:29618400-29639800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr18:29618400-29646800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:29618600-29642800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr18:29619400-29645400	Weak transcription	Fetal Stomach	stomach
15	chr18:29622800-29639800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:29625200-29629000	Weak transcription	Right Ventricle	heart
17	chr18:29626000-29657200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr18:29626200-29639800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:29626800-29630800	Enhancers	Primary B cells from cord blood	blood
20	chr18:29627000-29637600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr18:29627200-29632000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr18:29627400-29630800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr18:29627400-29637600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr18:29627600-29631400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr18:29627800-29631200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:29627800-29631400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr18:29627800-29631400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr18:29627800-29631400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr18:29628200-29629000	Enhancers	Fetal Muscle Trunk	muscle
30	chr18:29628200-29630200	Enhancers	Primary B cells from peripheral blood	blood
31	chr18:29628200-29630800	Enhancers	Fetal Intestine Small	intestine
32	chr18:29628200-29631200	Enhancers	Primary hematopoietic stem cells	blood
33	chr18:29628400-29629000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr18:29628400-29629000	Enhancers	Stomach Smooth Muscle	stomach
35	chr18:29628400-29629200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr18:29628400-29629200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr18:29628400-29629200	Enhancers	Colon Smooth Muscle	Colon
38	chr18:29628400-29629400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr18:29628400-29629400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr18:29628400-29629800	Enhancers	HepG2	liver
41	chr18:29628400-29630000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr18:29628400-29630000	Enhancers	Stomach Mucosa	stomach
43	chr18:29628400-29630200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr18:29628400-29630200	Enhancers	Adipose Nuclei	Adipose
45	chr18:29628400-29630200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr18:29628400-29630400	Enhancers	Duodenum Mucosa	Duodenum
47	chr18:29628400-29630600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr18:29628400-29631000	Enhancers	Fetal Intestine Large	intestine
49	chr18:29628400-29631000	Enhancers	Dnd41	blood
50	chr18:29628400-29631200	Enhancers	Primary neutrophils fromperipheralblood	blood

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