Variant report

Variant	rs794279
Chromosome Location	chr16:46713692-46713693
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	chr16:46701863..46703903-chr16:46713521..46715933,2	K562	blood:
2	chr16:46711146..46713693-chr16:46721499..46723929,2	K562	blood:

Variant related genes	Relation type
ENSG00000069329	Chromatin interaction
ENSG00000091651	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1009391	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs10468399	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651654	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs166161	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948661	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs17189741	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17792604	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183672	0.93[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869006	0.82[GIH][hapmap]
rs2341041	1.00[ASN][1000 genomes]
rs252721	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252722	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28174	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28184	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485103	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35444809	1.00[ASN][1000 genomes]
rs36310	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36462	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36464	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36471	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36472	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36476	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36481	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs36483	1.00[ASN][1000 genomes]
rs40163	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40355	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141491	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415018	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42461	0.81[EUR][1000 genomes]
rs4401068	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887592	1.00[ASN][1000 genomes]
rs4966606	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966616	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4967393	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59064826	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60500837	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66508669	1.00[ASN][1000 genomes]
rs66804065	1.00[ASN][1000 genomes]
rs67205347	1.00[ASN][1000 genomes]
rs67506574	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67611436	1.00[ASN][1000 genomes]
rs67789219	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68074363	1.00[ASN][1000 genomes]
rs698416	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs698418	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712816	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186662	0.85[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187475	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs7190713	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs7198951	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205668	1.00[ASN][1000 genomes]
rs72814883	1.00[ASN][1000 genomes]
rs72816835	1.00[ASN][1000 genomes]
rs72816877	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs8044684	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	1.00[ASN][1000 genomes]
rs8046748	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051017	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs808434	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs808780	0.93[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1060734	chr16:46463770-46768102	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active 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	38 gene(s)	inside rSNPs	diseases
3	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
6	esv1797185	chr16:46489836-46731413	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv428327	chr16:46556968-46718490	Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
14	nsv572536	chr16:46694649-46727385	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv962147	chr16:46704148-46713998	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1799771	chr16:46705343-46731413	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1792701	chr16:46709686-46751452	Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs794279	MYLK3	cis	cerebellum	SCAN
rs794279	SHCBP1	cis	parietal	SCAN
rs794279	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs794279	LONP2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46689200-46715800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr16:46689800-46716200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:46690400-46716200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:46691000-46714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr16:46691000-46715000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:46691000-46715600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr16:46691000-46716200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr16:46691000-46716800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:46691000-46718000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr16:46691200-46714800	Strong transcription	Liver	Liver
11	chr16:46691200-46716200	Strong transcription	Adipose Nuclei	Adipose
12	chr16:46691200-46716400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr16:46691200-46716800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:46691200-46717000	Strong transcription	Dnd41	blood
15	chr16:46691200-46717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:46692400-46716800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr16:46692600-46716200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:46692600-46717000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr16:46692800-46717400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr16:46693000-46715200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr16:46693000-46716800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr16:46694000-46716600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr16:46694000-46717600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr16:46694200-46716600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr16:46694200-46716800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:46694600-46716800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:46695000-46716400	Weak transcription	Stomach Mucosa	stomach
28	chr16:46697000-46716200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:46698600-46717800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr16:46698800-46715600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr16:46699000-46715600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:46700800-46714800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr16:46702400-46717600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:46702600-46715600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr16:46702600-46716400	Weak transcription	Fetal Heart	heart
36	chr16:46702600-46716800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:46702600-46722200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr16:46703400-46716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr16:46704200-46715600	Strong transcription	Fetal Lung	lung
40	chr16:46705000-46720000	Weak transcription	Fetal Brain Male	brain
41	chr16:46705000-46720600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr16:46705000-46720600	Weak transcription	Brain Substantia Nigra	brain
43	chr16:46705000-46721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr16:46705600-46721400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr16:46705800-46716200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr16:46705800-46720600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr16:46705800-46721400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr16:46705800-46721400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr16:46705800-46722200	Weak transcription	Aorta	Aorta
50	chr16:46706200-46715800	Strong transcription	HSMM	muscle

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