Variant report

Variant	rs9939383
Chromosome Location	chr16:12176120-12176121
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	chr16:12174212..12176270-chr16:12182353..12184871,2	K562	blood:

Variant related genes	Relation type
ENSG00000175604	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11075049	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639701	0.80[ASN][1000 genomes]
rs11642386	0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11648228	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11648468	0.93[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11648816	0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs12596549	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12596703	0.82[JPT][hapmap]
rs12599090	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12708745	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12708746	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708747	0.82[JPT][hapmap]
rs12926900	0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs13330399	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13331254	0.92[CHB][hapmap]
rs13333662	0.82[JPT][hapmap]
rs13336687	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13338070	0.89[AFR][1000 genomes]
rs16958964	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2175020	0.82[JPT][hapmap]
rs2457193	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28439695	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28667047	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350264	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350265	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350266	0.89[ASN][1000 genomes]
rs35053871	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35318501	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3851011	0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3851012	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3894905	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4780411	0.83[ASN][1000 genomes]
rs4781180	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs71385189	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7195019	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7200307	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8048589	0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8050180	1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]
rs8055516	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8059989	0.85[ASN][1000 genomes]
rs8062015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8063329	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9925009	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9939383	NUBP1	cis	parietal	SCAN
rs9939383	MYH11	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr16:12146000-12183400	Weak transcription	Fetal Intestine Large	intestine
4	chr16:12148000-12183400	Weak transcription	Fetal Lung	lung
5	chr16:12153400-12177200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
7	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
8	chr16:12157000-12181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:12157000-12181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:12157200-12183200	Weak transcription	NHLF	lung
11	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:12157800-12181400	Weak transcription	Right Ventricle	heart
13	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
14	chr16:12162200-12181400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:12163600-12181600	Weak transcription	Brain Substantia Nigra	brain
16	chr16:12163600-12183600	Weak transcription	Colon Smooth Muscle	Colon
17	chr16:12163800-12181600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr16:12167600-12185800	Weak transcription	HSMM	muscle
19	chr16:12169200-12176400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:12170000-12176800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr16:12170000-12178600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:12170000-12183400	Weak transcription	HepG2	liver
23	chr16:12170200-12183400	Weak transcription	Colonic Mucosa	Colon
24	chr16:12170400-12176800	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr16:12170400-12179600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr16:12170600-12182000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr16:12170800-12179200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr16:12171000-12179600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:12171400-12178000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr16:12171400-12180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr16:12171600-12180200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr16:12171800-12178400	Strong transcription	Adipose Nuclei	Adipose
33	chr16:12172200-12178000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:12172400-12176400	Strong transcription	NHDF-Ad	bronchial
35	chr16:12172400-12178600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:12172600-12176200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:12172600-12177800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr16:12172600-12178000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr16:12172600-12178000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr16:12172600-12178000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr16:12172600-12178000	Strong transcription	NHEK	skin
42	chr16:12172600-12178600	Strong transcription	Aorta	Aorta
43	chr16:12172600-12179200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:12172600-12179200	Strong transcription	Fetal Stomach	stomach
45	chr16:12172800-12176600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr16:12173000-12180800	Weak transcription	Gastric	stomach
47	chr16:12173000-12181600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr16:12173000-12181600	Weak transcription	Esophagus	oesophagus
49	chr16:12173000-12181600	Weak transcription	Right Atrium	heart
50	chr16:12173200-12178400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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