Variant report

Variant	rs11039416
Chromosome Location	chr11:47846711-47846712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10838747	0.81[ASN][1000 genomes]
rs10838748	0.81[ASN][1000 genomes]
rs10838757	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039342	0.81[ASN][1000 genomes]
rs11039355	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11039389	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039390	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039391	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039426	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039433	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602339	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11602395	0.80[ASN][1000 genomes]
rs11605774	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12361031	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12361256	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12364432	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12418852	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421210	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12785833	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787330	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12798109	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803191	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17788930	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2290850	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34128973	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614231	0.82[AMR][1000 genomes]
rs34910028	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34923397	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35805829	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35902101	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35985502	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752797	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752801	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752873	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105282	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7120333	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130758	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927771	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7947730	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9909	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11039416	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039416	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039416	C1QTNF4	cis	Whole Blood	GTEx
rs11039416	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039416	C1QTNF4	cis	lung	GTEx
rs11039416	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs11039416	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039416	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
3	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47796200-47849400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:47796200-47849800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:47796200-47850200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:47796400-47848800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:47796400-47848800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:47796400-47850600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:47796400-47858800	Strong transcription	Liver	Liver
17	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:47796600-47850800	Strong transcription	Hela-S3	cervix
19	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:47796800-47852000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:47798000-47868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:47798400-47864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:47798600-47851600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:47807000-47865600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr11:47812400-47849000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:47814600-47850000	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:47815200-47851800	Strong transcription	Fetal Intestine Large	intestine
28	chr11:47817600-47851400	Strong transcription	Fetal Brain Female	brain
29	chr11:47820000-47864800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:47823000-47854600	Weak transcription	Fetal Heart	heart
31	chr11:47823200-47854800	Weak transcription	Aorta	Aorta
32	chr11:47831800-47849600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:47831800-47850800	Strong transcription	GM12878-XiMat	blood
34	chr11:47831800-47868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:47833800-47853200	Weak transcription	Gastric	stomach
36	chr11:47833800-47854600	Weak transcription	Esophagus	oesophagus
37	chr11:47834000-47853600	Weak transcription	NHLF	lung
38	chr11:47834200-47854000	Weak transcription	Right Ventricle	heart
39	chr11:47834200-47855200	Weak transcription	Psoas Muscle	Psoas
40	chr11:47834600-47856000	Weak transcription	Colonic Mucosa	Colon
41	chr11:47835000-47853600	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:47835400-47854000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:47836600-47848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:47837200-47853600	Weak transcription	Spleen	Spleen
45	chr11:47837200-47857200	Weak transcription	Small Intestine	intestine
46	chr11:47837600-47850200	Weak transcription	Fetal Brain Male	brain
47	chr11:47837800-47849400	Strong transcription	Fetal Intestine Small	intestine
48	chr11:47837800-47854000	Weak transcription	NHEK	skin
49	chr11:47838400-47847400	Strong transcription	Thymus	Thymus
50	chr11:47839000-47851000	Strong transcription	Dnd41	blood

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