Variant report

Variant	rs35805829
Chromosome Location	chr11:47805478-47805479
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	chr11:47789258..47792830-chr11:47805227..47807948,3	K562	blood:
2	chr11:47788391..47791248-chr11:47803262..47807448,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10838747	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838748	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838757	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039342	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039348	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039355	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039389	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039390	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039391	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039416	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039426	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039433	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11602339	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11602395	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11604825	0.80[ASN][1000 genomes]
rs11605774	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361031	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12364432	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12418852	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421210	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12785833	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12787112	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12787330	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798109	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12803191	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17788930	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290850	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34128973	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34910028	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34923397	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35902101	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35985502	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752797	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752873	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105282	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7120333	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130758	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7927771	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7947730	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs35805829	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs35805829	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs35805829	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs35805829	C1QTNF4	cis	Whole Blood	GTEx
rs35805829	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs35805829	C1QTNF4	cis	Muscle Skeletal	GTEx
rs35805829	C1QTNF4	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790000-47806800	Weak transcription	Esophagus	oesophagus
2	chr11:47790000-47837800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:47790800-47832200	Weak transcription	Small Intestine	intestine
5	chr11:47795200-47845600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
7	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:47795600-47808200	Strong transcription	Primary B cells from cord blood	blood
9	chr11:47795600-47810600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47796000-47812800	Strong transcription	Fetal Muscle Leg	muscle
11	chr11:47796000-47816800	Strong transcription	GM12878-XiMat	blood
12	chr11:47796200-47808200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr11:47796200-47810400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:47796200-47811200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:47796200-47813600	Strong transcription	Adipose Nuclei	Adipose
16	chr11:47796200-47834000	Strong transcription	Fetal Stomach	stomach
17	chr11:47796200-47837800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:47796200-47843600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:47796200-47845200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr11:47796200-47845600	Strong transcription	Placenta	Placenta
21	chr11:47796200-47849400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:47796200-47849800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:47796200-47850200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:47796400-47807400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:47796400-47814400	Strong transcription	Fetal Intestine Large	intestine
32	chr11:47796400-47824800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:47796400-47844000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:47796400-47848800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:47796400-47848800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:47796400-47850600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:47796400-47858800	Strong transcription	Liver	Liver
38	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:47796600-47810200	Strong transcription	Lung	lung
40	chr11:47796600-47843600	Strong transcription	Brain Germinal Matrix	brain
41	chr11:47796600-47850800	Strong transcription	Hela-S3	cervix
42	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:47796800-47809600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:47796800-47810200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:47796800-47810400	Strong transcription	Osteobl	bone
46	chr11:47796800-47811200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:47796800-47813200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:47796800-47813800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:47796800-47837600	Strong transcription	Dnd41	blood
50	chr11:47796800-47843800	Strong transcription	Primary B cells from peripheral blood	blood

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