Variant report

Variant	rs4873546
Chromosome Location	chr8:48576665-48576666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48575452..48577775-chr8:48649068..48651275,2	K562	blood:
2	chr8:48571242..48574172-chr8:48576074..48578084,2	K562	blood:

Variant related genes	Relation type
ENSG00000164808	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10094128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10109113	0.82[EUR][1000 genomes]
rs10441581	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10958058	0.81[CEU][hapmap]
rs1106607	0.81[CEU][hapmap]
rs11784823	0.81[CEU][hapmap]
rs12544329	0.81[CEU][hapmap]
rs12549996	0.81[CEU][hapmap]
rs12674784	0.87[JPT][hapmap]
rs13279327	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[YRI][hapmap]
rs1542721	0.87[JPT][hapmap]
rs16930163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16930230	0.87[JPT][hapmap]
rs2029239	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2130413	0.81[CEU][hapmap]
rs4436571	0.86[EUR][1000 genomes]
rs4486659	0.85[EUR][1000 genomes]
rs4594029	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4608108	0.81[CEU][hapmap]
rs4873368	0.81[CEU][hapmap]
rs4873386	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4873395	0.81[CEU][hapmap]
rs4873446	0.87[EUR][1000 genomes]
rs4873463	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs4873478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6472452	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap]
rs6982620	0.81[CEU][hapmap]
rs6986054	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462209	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827571	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7830859	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7833589	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap]
rs7842068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876915	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4873546	KIAA0146	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48571600-48577000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:48572600-48577000	Enhancers	Placenta	Placenta
3	chr8:48572800-48578400	Weak transcription	Primary B cells from cord blood	blood
4	chr8:48573000-48577000	Enhancers	Lung	lung
5	chr8:48573000-48582600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr8:48573200-48589200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr8:48573400-48579200	Weak transcription	A549	lung
8	chr8:48573600-48576800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr8:48573600-48578800	Weak transcription	Adipose Nuclei	Adipose
10	chr8:48573600-48582200	Weak transcription	Spleen	Spleen
11	chr8:48573800-48578400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:48574000-48577200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:48574200-48581800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:48574200-48589600	Weak transcription	Fetal Intestine Large	intestine
15	chr8:48574400-48577000	Enhancers	Fetal Heart	heart
16	chr8:48574400-48591000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr8:48574400-48592600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr8:48574800-48580200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr8:48574800-48581200	Weak transcription	Brain Anterior Caudate	brain
20	chr8:48574800-48581200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr8:48574800-48581600	Weak transcription	Aorta	Aorta
22	chr8:48574800-48588200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:48574800-48588400	Weak transcription	NHLF	lung
24	chr8:48574800-48595800	Weak transcription	Ovary	ovary
25	chr8:48575000-48580400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr8:48575000-48581200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr8:48575000-48581600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:48575000-48589400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr8:48575200-48578800	Weak transcription	Liver	Liver
30	chr8:48575400-48576800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:48575600-48576800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr8:48575600-48576800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr8:48575600-48576800	Enhancers	Pancreas	Pancrea
34	chr8:48575600-48576800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr8:48575600-48576800	Enhancers	NHDF-Ad	bronchial
36	chr8:48575600-48577000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr8:48575600-48592000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr8:48575800-48576800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr8:48575800-48576800	Enhancers	Fetal Brain Female	brain
40	chr8:48575800-48576800	Enhancers	Psoas Muscle	Psoas
41	chr8:48575800-48576800	Enhancers	Right Atrium	heart
42	chr8:48575800-48576800	Enhancers	Right Ventricle	heart
43	chr8:48575800-48577000	Enhancers	Left Ventricle	heart
44	chr8:48575800-48580200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:48575800-48581200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr8:48576000-48581400	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:48576000-48589200	Weak transcription	Esophagus	oesophagus
48	chr8:48576000-48592800	Weak transcription	Small Intestine	intestine
49	chr8:48576000-48595800	Weak transcription	Gastric	stomach
50	chr8:48576200-48580600	Weak transcription	HSMMtube	muscle

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