Variant report

Variant	rs12794570
Chromosome Location	chr11:47658314-47658315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47648151..47655137-chr11:47656071..47661932,11	K562	blood:
2	chr11:47652437..47655137-chr11:47656639..47658574,2	K562	blood:
3	chr11:47648507..47652310-chr11:47658295..47660637,4	K562	blood:
4	chr11:47655594..47657226-chr11:47658278..47659810,2	K562	blood:

Variant related genes	Relation type
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1064608	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838747	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838748	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838757	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.83[ASN][1000 genomes]
rs11039308	0.97[ASN][1000 genomes]
rs11039324	0.91[ASN][1000 genomes]
rs11039342	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039348	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039355	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11602339	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11602395	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11604825	0.82[ASN][1000 genomes]
rs12361031	0.80[ASN][1000 genomes]
rs12363232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12419507	0.92[ASN][1000 genomes]
rs12419692	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421210	0.82[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787646	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798028	0.84[ASN][1000 genomes]
rs12798346	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12799623	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12803191	0.82[ASN][1000 genomes]
rs1317149	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs17788930	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2030166	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290850	0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs34910028	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34923397	0.81[ASN][1000 genomes]
rs34958982	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3817334	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3817335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752845	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752857	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400411	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59360790	0.95[ASN][1000 genomes]
rs66749409	0.85[ASN][1000 genomes]
rs7105282	0.95[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs7124681	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7927771	0.95[CEU][hapmap];0.80[ASN][1000 genomes]
rs7928842	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7947730	0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs9909	0.95[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]

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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	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
4	esv3439101	chr11:47657065-47660300	Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12794570	Hs.6637	cis	multi-tissue	Pritchard
rs12794570	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12794570	SPI1	cis	multi-tissue	Pritchard
rs12794570	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12794570	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12794570	C1QTNF4	cis	multi-tissue	Pritchard
rs12794570	C1QTNF4	cis	lung	GTEx
rs12794570	C1QTNF4	cis	Artery Tibial	GTEx
rs12794570	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12794570	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12794570	C1QTNF4	cis	Whole Blood	GTEx
rs12794570	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47636600-47661400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:47637600-47660800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:47637600-47661200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:47637800-47660400	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:47637800-47661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:47637800-47661000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:47638000-47661400	Strong transcription	Fetal Thymus	thymus
9	chr11:47638000-47661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47638200-47661200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:47638200-47661200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr11:47638200-47661600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:47638200-47661600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:47638400-47660400	Strong transcription	Dnd41	blood
15	chr11:47638400-47661200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:47638800-47661600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:47639000-47661200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:47639000-47661400	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:47639000-47662600	Weak transcription	Stomach Mucosa	stomach
20	chr11:47639600-47661200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr11:47640000-47661000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:47640600-47661400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:47640800-47661400	Strong transcription	Fetal Intestine Small	intestine
27	chr11:47640800-47661400	Strong transcription	Fetal Stomach	stomach
28	chr11:47641800-47659200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:47641800-47661200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:47641800-47661600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:47642000-47661400	Strong transcription	Placenta	Placenta
32	chr11:47642000-47661800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:47643400-47661200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:47644000-47661600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:47646800-47662600	Weak transcription	Aorta	Aorta
36	chr11:47648200-47662800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:47648200-47663200	Weak transcription	Gastric	stomach
38	chr11:47648400-47662800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:47649200-47662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:47653400-47661600	Weak transcription	Pancreas	Pancrea
41	chr11:47653400-47662600	Weak transcription	Psoas Muscle	Psoas
42	chr11:47653600-47662200	Weak transcription	Fetal Brain Male	brain
43	chr11:47653600-47662200	Weak transcription	Fetal Heart	heart
44	chr11:47653800-47662400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:47654000-47660800	Strong transcription	Liver	Liver
46	chr11:47654000-47661200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:47654400-47658800	Strong transcription	Lung	lung
48	chr11:47654400-47661200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:47654400-47661400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:47654600-47661200	Strong transcription	Thymus	Thymus

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