Variant report

Variant	rs8048589
Chromosome Location	chr16:12185810-12185811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr16:12185519-12185886	K562	blood:	n/a	chr16:12185685-12185700
2	BACH1	chr16:12185512-12185901	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFK	chr16:12185580-12185878	HepG2	liver:	n/a	chr16:12185685-12185700
4	MAFF	chr16:12185508-12185873	K562	blood:	n/a	chr16:12185683-12185701
5	FOXA2	chr16:12185557-12185836	HepG2	liver:	n/a	n/a
6	MAFK	chr16:12185624-12185882	H1-hESC	embryonic stem cell:	n/a	chr16:12185685-12185700
7	MAFF	chr16:12185574-12185871	HepG2	liver:	n/a	chr16:12185683-12185701
8	BACH1	chr16:12185551-12185876	K562	blood:	n/a	n/a
9	ZNF384	chr16:12185435-12185854	K562	blood:	n/a	n/a
10	MAFK	chr16:12185524-12185872	HepG2	liver:	n/a	chr16:12185685-12185700

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12183674..12186424-chr16:12186757..12189168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175604	TF binding region
ENSG00000261293	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11075049	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs11075054	0.81[ASN][1000 genomes]
rs11639701	0.94[ASN][1000 genomes]
rs11642033	0.85[ASN][1000 genomes]
rs11642386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11646458	0.88[ASN][1000 genomes]
rs11646539	0.81[ASN][1000 genomes]
rs11646584	0.85[ASN][1000 genomes]
rs11647572	0.82[ASN][1000 genomes]
rs11648228	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648468	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648816	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596703	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12599090	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12599793	0.81[ASN][1000 genomes]
rs12708746	0.80[ASN][1000 genomes]
rs12708747	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12926900	0.81[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12929519	0.85[ASN][1000 genomes]
rs13333662	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs13336687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175020	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2457193	0.86[ASN][1000 genomes]
rs28439695	0.87[ASN][1000 genomes]
rs28667047	0.86[ASN][1000 genomes]
rs2869808	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs350233	0.82[JPT][hapmap]
rs350264	0.86[ASN][1000 genomes]
rs350265	0.82[ASN][1000 genomes]
rs350266	0.82[ASN][1000 genomes]
rs35053871	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35318501	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35542345	0.85[ASN][1000 genomes]
rs3851011	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851012	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs3894905	0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap]
rs4780411	0.98[ASN][1000 genomes]
rs4781180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs71385189	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200307	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050180	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs8055516	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8059989	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062015	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8063329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925009	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9935284	0.81[ASN][1000 genomes]
rs9936270	0.80[ASN][1000 genomes]
rs9939383	0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Homeostasis model assessment of insulin resistance (interaction)	24204828	GWAS catalog
Fasting insulin (interaction)	24204828	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8048589	TNFRSF17	cis	parietal	SCAN
rs8048589	TNFRSF17	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:12178600-12199600	Weak transcription	Aorta	Aorta
3	chr16:12182200-12188600	Weak transcription	Fetal Brain Male	brain
4	chr16:12183200-12186200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr16:12183800-12186000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:12183800-12186000	Weak transcription	Fetal Heart	heart
7	chr16:12183800-12186000	Weak transcription	GM12878-XiMat	blood
8	chr16:12183800-12189200	Weak transcription	Pancreas	Pancrea
9	chr16:12184000-12186000	Weak transcription	Brain Angular Gyrus	brain
10	chr16:12184000-12189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:12184000-12189200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:12184000-12189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr16:12184000-12189200	Weak transcription	Liver	Liver
14	chr16:12184000-12189200	Weak transcription	Colon Smooth Muscle	Colon
15	chr16:12184000-12189200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:12184000-12189400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:12184000-12191600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:12184200-12186600	Weak transcription	Right Atrium	heart
19	chr16:12184200-12187000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12184200-12189000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:12184200-12189000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr16:12184200-12189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:12184200-12189200	Weak transcription	Fetal Intestine Large	intestine
25	chr16:12184200-12190400	Enhancers	Thymus	Thymus
26	chr16:12184200-12192200	Weak transcription	Gastric	stomach
27	chr16:12184200-12193000	Enhancers	Fetal Thymus	thymus
28	chr16:12184400-12186000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr16:12184400-12186000	Weak transcription	Stomach Mucosa	stomach
30	chr16:12184400-12186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:12184400-12187200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr16:12184400-12188200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:12184400-12189200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr16:12184600-12186000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr16:12184600-12186200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr16:12184600-12186200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr16:12184600-12187000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr16:12184600-12188800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr16:12184600-12188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr16:12184600-12189200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr16:12184800-12186600	Enhancers	K562	blood
43	chr16:12185000-12186600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:12185000-12187000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr16:12185000-12187000	Enhancers	NHDF-Ad	bronchial
46	chr16:12185000-12187400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr16:12185000-12188200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:12185200-12186000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr16:12185200-12186400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr16:12185200-12186800	Strong transcription	NHEK	skin

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