Variant report

Variant	rs3817334
Chromosome Location	chr11:47650993-47650994
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	chr11:47648151..47655137-chr11:47656071..47661932,11	K562	blood:
2	chr11:47648507..47652310-chr11:47658295..47660637,4	K562	blood:

Variant related genes	Relation type
ENSG00000109919	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1064608	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10838738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs10838747	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10838748	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs10838757	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039308	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039324	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039342	0.86[ASN][1000 genomes]
rs11039348	0.83[ASN][1000 genomes]
rs11039355	0.81[ASN][1000 genomes]
rs11602339	0.80[ASN][1000 genomes]
rs11602395	0.85[ASN][1000 genomes]
rs11604680	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11604825	0.82[ASN][1000 genomes]
rs12361031	0.80[ASN][1000 genomes]
rs12363232	0.95[ASN][1000 genomes]
rs12419507	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419692	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs12421210	0.82[ASN][1000 genomes]
rs12787112	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12787646	0.95[ASN][1000 genomes]
rs12794570	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12798028	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12798346	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs12799623	0.92[ASN][1000 genomes]
rs12803191	0.82[ASN][1000 genomes]
rs1317149	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs17788930	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2030166	0.84[ASN][1000 genomes]
rs2290850	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2868459	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34910028	0.83[ASN][1000 genomes]
rs34923397	0.81[ASN][1000 genomes]
rs34958982	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs3817335	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4752845	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs4752857	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56400411	0.83[ASN][1000 genomes]
rs59360790	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66749409	0.85[ASN][1000 genomes]
rs7105282	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7124681	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7927771	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs7928842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7947730	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs9909	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Body mass index	20935630	GWAS catalog

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs3817334	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs3817334	SPI1	cis	multi-tissue	Pritchard
rs3817334	SLC35C1	cis	parietal	SCAN
rs3817334	SPI1	cis	Lymphoblastoid	GTEx
rs3817334	C1QTNF4	cis	multi-tissue	Pritchard
rs3817334	CRY2	cis	parietal	SCAN
rs3817334	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs3817334		cis	Lymphoblastoid	GTEx
rs3817334	MTCH2	cis	brain	seeQTL
rs3817334	C1QTNF4	cis	lymphoblastoid	seeQTL
rs3817334	PSMC3	cis	cerebellum	SCAN
rs3817334	MTCH2	cis	cerebellum	SCAN
rs3817334	NR1H3	cis	multi-tissue	Pritchard
rs3817334	SLC39A13	cis	cerebellum	SCAN
rs3817334	C1QTNF4	cis	Muscle Skeletal	GTEx
rs3817334	MADD	cis	cerebellum	SCAN
rs3817334	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs3817334	SPI1	cis	lymphoblastoid	seeQTL
rs3817334	MYBPC3	cis	multi-tissue	Pritchard
rs3817334	Hs.6637	cis	multi-tissue	Pritchard

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	chr11:47636800-47653800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:47637000-47653400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:47637600-47653200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:47637600-47653200	Strong transcription	Liver	Liver
6	chr11:47637600-47657200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr11:47637600-47660800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:47637600-47661200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:47637800-47653200	Strong transcription	Left Ventricle	heart
11	chr11:47637800-47660400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:47637800-47661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:47637800-47661000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:47638000-47661400	Strong transcription	Fetal Thymus	thymus
15	chr11:47638000-47661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:47638200-47652800	Strong transcription	Hela-S3	cervix
17	chr11:47638200-47661200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:47638200-47661200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr11:47638200-47661600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:47638200-47661600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:47638400-47653400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr11:47638400-47653800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:47638400-47654000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:47638400-47660400	Strong transcription	Dnd41	blood
25	chr11:47638400-47661200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:47638600-47653600	Strong transcription	Primary B cells from cord blood	blood
27	chr11:47638600-47654000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr11:47638600-47657200	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:47638800-47661600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:47639000-47651400	Strong transcription	K562	blood
31	chr11:47639000-47658000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr11:47639000-47661200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:47639000-47661400	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:47639000-47662600	Weak transcription	Stomach Mucosa	stomach
35	chr11:47639200-47653800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:47639200-47657600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr11:47639400-47655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:47639600-47661200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:47639800-47657600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:47640000-47653800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:47640000-47661000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:47640200-47652400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:47640200-47661200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:47640400-47651200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:47640400-47653800	Strong transcription	Fetal Brain Female	brain
48	chr11:47640600-47651200	Strong transcription	Brain Germinal Matrix	brain
49	chr11:47640600-47653400	Strong transcription	Lung	lung
50	chr11:47640600-47661400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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