Variant report

Variant	rs6554
Chromosome Location	chr19:18685964-18685965
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18629832..18635572-chr19:18680910..18686315,11	K562	blood:
2	chr19:18528984..18533499-chr19:18684426..18687340,4	MCF-7	breast:
3	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
4	chr19:18585110..18587475-chr19:18684025..18685972,2	MCF-7	breast:
5	chr19:18668612..18670629-chr19:18685047..18687123,3	MCF-7	breast:
6	chr19:18685737..18689884-chr19:18697340..18702135,5	MCF-7	breast:
7	chr19:18625937..18627483-chr19:18684789..18686553,2	K562	blood:

Variant related genes	Relation type
ENSG00000130511	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000006015	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10409392	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs10425018	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043192	0.81[JPT][hapmap]
rs11086114	0.87[ASN][1000 genomes]
rs11086116	0.82[ASN][1000 genomes]
rs11667551	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672297	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12150991	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608925	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609505	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468475	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862645	0.81[JPT][hapmap]
rs2057649	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2058077	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2079015	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2079016	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238650	0.81[JPT][hapmap]
rs2283616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302055	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2314664	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2314665	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2314666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2314667	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28451415	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28711754	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3170474	0.85[JPT][hapmap]
rs35867875	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35875334	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36050418	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761032	0.81[JPT][hapmap]
rs3761034	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761036	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795028	1.00[YRI][hapmap]
rs3803917	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4629093	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808137	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808821	0.92[ASN][1000 genomes]
rs4808839	0.81[JPT][hapmap]
rs55724121	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55888366	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58782998	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59798925	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137086	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709679	0.81[JPT][hapmap]
rs7247557	0.80[ASN][1000 genomes]
rs7250192	0.81[JPT][hapmap]
rs7250623	0.90[JPT][hapmap]
rs7253088	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7254004	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256319	0.85[JPT][hapmap]
rs7258480	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109364	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs8110371	0.86[EUR][1000 genomes]
rs8110374	0.86[EUR][1000 genomes]
rs916791	0.81[JPT][hapmap]

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	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6554	UBA52	cis	lymphoblastoid	seeQTL
rs6554	NDUFA13	cis	parietal	SCAN
rs6554	NCAN	cis	cerebellum	SCAN
rs6554	GATAD2A	cis	cerebellum	SCAN
rs6554	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18683800-18687800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18684200-18687200	Strong transcription	Aorta	Aorta
3	chr19:18684200-18687200	Strong transcription	Rectal Smooth Muscle	rectum
4	chr19:18684200-18687400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:18684200-18687600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:18684200-18688000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:18684200-18688800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr19:18684200-18688800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:18684200-18689400	Weak transcription	Fetal Heart	heart
10	chr19:18684200-18690200	Strong transcription	Fetal Brain Female	brain
11	chr19:18684400-18686200	Weak transcription	Fetal Kidney	kidney
12	chr19:18684400-18687400	Strong transcription	Fetal Lung	lung
13	chr19:18684400-18687800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr19:18684400-18688200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:18684400-18688600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:18684400-18688800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:18684400-18688800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:18684400-18688800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:18684400-18688800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:18684400-18688800	Strong transcription	Thymus	Thymus
21	chr19:18684400-18689000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:18684400-18689200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:18684400-18689400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:18684400-18689400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:18684400-18689400	Strong transcription	Liver	Liver
26	chr19:18684400-18689600	Strong transcription	Fetal Stomach	stomach
27	chr19:18684400-18689600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:18684400-18689800	Strong transcription	Brain Anterior Caudate	brain
29	chr19:18684400-18689800	Strong transcription	Brain Hippocampus Middle	brain
30	chr19:18684400-18689800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr19:18684400-18690200	Strong transcription	Primary T cells from cord blood	blood
32	chr19:18684400-18691400	Weak transcription	Fetal Brain Male	brain
33	chr19:18684400-18698600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:18684600-18686000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:18684600-18686200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:18684600-18686400	Genic enhancers	K562	blood
37	chr19:18684600-18687000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:18684600-18687000	Strong transcription	HepG2	liver
39	chr19:18684600-18687200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:18684600-18687200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:18684600-18687200	Strong transcription	HSMMtube	muscle
42	chr19:18684600-18687400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr19:18684600-18687400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:18684600-18687400	Strong transcription	Brain Substantia Nigra	brain
45	chr19:18684600-18687400	Strong transcription	HUVEC	blood vessel
46	chr19:18684600-18687600	Strong transcription	HSMM	muscle
47	chr19:18684600-18687800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:18684600-18687800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:18684600-18688000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:18684600-18688200	Strong transcription	Brain Cingulate Gyrus	brain

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