Variant report

Variant	rs11075049
Chromosome Location	chr16:12173539-12173540
allele	A/G
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	SPI1	chr16:12173353-12173597	GM12891	blood:	n/a	n/a
2	MXI1	chr16:12173516-12173551	K562	blood:	n/a	n/a
3	FOXA1	chr16:12173380-12173626	T-47D	breast:	n/a	chr16:12173485-12173497

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12069629..12072468-chr16:12173207..12175470,2	MCF-7	breast:

Variant related genes	Relation type
RPS23P6	TF binding region
ENSG00000260488	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000234719	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11642386	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs11648228	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11648468	0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11648816	0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs12596549	0.81[ASN][1000 genomes]
rs12596703	0.82[JPT][hapmap]
rs12599090	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12708745	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12708746	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708747	0.82[JPT][hapmap]
rs12926900	0.94[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs13330399	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs13331254	0.92[CHB][hapmap]
rs13333662	0.82[JPT][hapmap]
rs13336687	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13338070	0.92[AFR][1000 genomes]
rs16958964	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2175020	0.82[JPT][hapmap]
rs2457193	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28439695	0.93[ASN][1000 genomes]
rs28667047	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869808	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350264	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350265	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350266	0.87[ASN][1000 genomes]
rs35053871	0.81[ASN][1000 genomes]
rs35318501	0.81[AMR][1000 genomes]
rs3851011	0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3851012	0.94[JPT][hapmap]
rs3894905	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4781180	0.94[JPT][hapmap]
rs71385189	0.81[ASN][1000 genomes]
rs7195019	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7200307	0.81[ASN][1000 genomes]
rs8048589	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs8050180	1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs8055516	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8059989	0.81[ASN][1000 genomes]
rs8062015	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8063329	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9925009	0.82[JPT][hapmap]
rs9939383	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]

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
rs11075049	MYH11	cis	cerebellum	SCAN
rs11075049	NUBP1	cis	parietal	SCAN

Chromatin state (count:102 , 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	chr16:12157000-12175800	Weak transcription	Fetal Kidney	kidney
9	chr16:12157000-12181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:12157000-12181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:12157200-12173800	Weak transcription	Osteobl	bone
12	chr16:12157200-12183200	Weak transcription	NHLF	lung
13	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:12157800-12174000	Weak transcription	Left Ventricle	heart
15	chr16:12157800-12181400	Weak transcription	Right Ventricle	heart
16	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
17	chr16:12160600-12174000	Weak transcription	Spleen	Spleen
18	chr16:12162200-12181400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:12163600-12181600	Weak transcription	Brain Substantia Nigra	brain
20	chr16:12163600-12183600	Weak transcription	Colon Smooth Muscle	Colon
21	chr16:12163800-12181600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr16:12167600-12185800	Weak transcription	HSMM	muscle
23	chr16:12168800-12173800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr16:12168800-12174000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr16:12169200-12176400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr16:12169400-12173600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr16:12170000-12173600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:12170000-12176800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr16:12170000-12178600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:12170000-12183400	Weak transcription	HepG2	liver
31	chr16:12170200-12183400	Weak transcription	Colonic Mucosa	Colon
32	chr16:12170400-12176800	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr16:12170400-12179600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr16:12170600-12182000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:12170800-12176000	Strong transcription	Fetal Muscle Leg	muscle
36	chr16:12170800-12179200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:12171000-12179600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:12171200-12174000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:12171400-12178000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr16:12171400-12180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:12171600-12180200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr16:12171800-12175600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr16:12171800-12178400	Strong transcription	Adipose Nuclei	Adipose
44	chr16:12172200-12173800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr16:12172200-12178000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:12172400-12173600	Strong transcription	Brain Hippocampus Middle	brain
47	chr16:12172400-12173800	Enhancers	Stomach Mucosa	stomach
48	chr16:12172400-12174600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr16:12172400-12175600	Strong transcription	Pancreas	Pancrea
50	chr16:12172400-12176400	Strong transcription	NHDF-Ad	bronchial

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