Variant report

Variant	rs12094547
Chromosome Location	chr1:93578129-93578130
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	chr1:93577366..93579153-chr1:93581090..93583964,2	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11164874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164878	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164882	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11586323	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12057476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12066315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12067005	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12087466	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1414367	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17131699	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391227	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2749735	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783492	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783498	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2783506	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815408	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815409	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815410	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815411	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815412	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2815413	0.82[EUR][1000 genomes]
rs2815414	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36057148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505531	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs506556	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs522999	0.82[EUR][1000 genomes]
rs546	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55701931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs581825	0.81[EUR][1000 genomes]
rs615416	0.82[EUR][1000 genomes]
rs658877	0.82[EUR][1000 genomes]
rs667680	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs671559	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71510760	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs797660	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv508404	chr1:93547383-93580012	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12094547	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12094547	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12094547	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs12094547	RP4-717I23.3	cis	Thyroid	GTEx
rs12094547	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12094547	RP4-717I23.3	cis	Artery Aorta	GTEx
rs12094547	RP4-717I23.3	cis	Whole Blood	GTEx
rs12094547	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12094547	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12094547	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12094547	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12094547	RP4-717I23.3	cis	Stomach	GTEx
rs12094547	RP4-717I23.3	cis	lung	GTEx
rs12094547	RP4-717I23.3	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93545800-93578400	Weak transcription	Pancreas	Pancrea
2	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
3	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
7	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
8	chr1:93548000-93601800	Weak transcription	NHLF	lung
9	chr1:93548200-93578400	Weak transcription	Lung	lung
10	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
11	chr1:93549000-93582400	Weak transcription	HMEC	breast
12	chr1:93549000-93582800	Weak transcription	NHEK	skin
13	chr1:93551400-93579800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:93551600-93578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:93551800-93579800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:93552000-93580000	Weak transcription	NH-A	brain
17	chr1:93555400-93581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:93559400-93581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:93560200-93581600	Weak transcription	Brain Anterior Caudate	brain
20	chr1:93563400-93582000	Weak transcription	Esophagus	oesophagus
21	chr1:93564000-93581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
23	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
24	chr1:93570000-93582200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:93570200-93581600	Weak transcription	Ovary	ovary
26	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
27	chr1:93571600-93578400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:93571600-93581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
30	chr1:93572800-93580400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:93573000-93580600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:93573400-93578400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:93573600-93578400	Weak transcription	Thymus	Thymus
35	chr1:93573600-93580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:93573600-93581000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:93573800-93578400	Weak transcription	Fetal Stomach	stomach
39	chr1:93573800-93580000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:93573800-93582000	Weak transcription	Brain Germinal Matrix	brain
41	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
42	chr1:93574000-93578400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:93574000-93578600	Weak transcription	Liver	Liver
44	chr1:93574200-93578400	Weak transcription	Fetal Intestine Small	intestine
45	chr1:93574200-93580400	Weak transcription	Placenta	Placenta
46	chr1:93574200-93581200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:93574200-93581600	Weak transcription	Fetal Brain Female	brain
48	chr1:93574200-93582600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:93574400-93578400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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