Variant report

Variant	rs12787330
Chromosome Location	chr11:47812311-47812312
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	chr11:47811479..47814279-chr11:47822398..47824365,2	K562	blood:
2	chr11:47810236..47812634-chr11:47815577..47817820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271543	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10838747	0.84[ASN][1000 genomes]
rs10838748	0.84[ASN][1000 genomes]
rs10838757	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039342	0.84[ASN][1000 genomes]
rs11039348	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039355	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039389	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039390	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039391	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11602395	0.82[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];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12364432	0.83[AMR][1000 genomes];0.85[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];0.88[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	0.82[ASN][1000 genomes]
rs12798109	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12803191	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17788930	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290850	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34923397	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35805829	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902101	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[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];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105282	0.86[AFR][1000 genomes];0.94[AMR][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];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7927771	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7947730	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12787330	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12787330	C1QTNF4	cis	Whole Blood	GTEx
rs12787330	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12787330	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12787330	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12787330	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12787330	C1QTNF4	cis	Artery Tibial	GTEx
rs12787330	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12787330	C1QTNF4	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790000-47837800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47790800-47832200	Weak transcription	Small Intestine	intestine
4	chr11:47795200-47845600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
6	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:47796000-47812800	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:47796000-47816800	Strong transcription	GM12878-XiMat	blood
9	chr11:47796200-47813600	Strong transcription	Adipose Nuclei	Adipose
10	chr11:47796200-47834000	Strong transcription	Fetal Stomach	stomach
11	chr11:47796200-47837800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:47796200-47843600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:47796200-47845200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:47796200-47845600	Strong transcription	Placenta	Placenta
15	chr11:47796200-47849400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:47796200-47849800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:47796200-47850200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:47796400-47814400	Strong transcription	Fetal Intestine Large	intestine
25	chr11:47796400-47824800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:47796400-47844000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:47796400-47848800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:47796400-47848800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:47796400-47850600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:47796400-47858800	Strong transcription	Liver	Liver
31	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:47796600-47843600	Strong transcription	Brain Germinal Matrix	brain
33	chr11:47796600-47850800	Strong transcription	Hela-S3	cervix
34	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:47796800-47813200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:47796800-47813800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:47796800-47837600	Strong transcription	Dnd41	blood
38	chr11:47796800-47843800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:47796800-47852000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:47798000-47868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:47798400-47837800	Strong transcription	Thymus	Thymus
42	chr11:47798400-47845200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:47798400-47864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:47798600-47812600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr11:47798600-47813200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:47798600-47819000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:47798600-47819000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:47798600-47851600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:47798800-47813600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:47798800-47816400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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