Variant report

Variant	rs3740686
Chromosome Location	chr11:47376363-47376364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr11:47376355-47377350	IMR90	lung:	n/a	chr11:47377117-47377127
2	FOXA1	chr11:47376177-47376433	HepG2	liver:	n/a	n/a
3	CTCF	chr11:47376309-47377682	A549	lung:	n/a	n/a
4	HCFC1	chr11:47375283-47378502	Hela-S3	cervix:	n/a	n/a
5	FOXA1	chr11:47376073-47376556	HepG2	liver:	n/a	n/a
6	CTCF	chr11:47376058-47377990	SK-N-SH	brain:	n/a	n/a
7	FOXA2	chr11:47376177-47376414	HepG2	liver:	n/a	n/a
8	POLR2A	chr11:47374127-47379189	HL-60	blood:	n/a	n/a
9	FOXA2	chr11:47376188-47376425	A549	lung:	n/a	n/a
10	POLR2A	chr11:47375214-47379216	HL-60	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47366884..47369322-chr11:47374735..47376976,2	K562	blood:
2	chr11:47181895..47183396-chr11:47375701..47377914,2	K562	blood:
3	chr11:47375459..47378280-chr11:47382815..47386328,3	K562	blood:
4	chr11:47375322..47377649-chr11:47398628..47401440,2	K562	blood:
5	chr11:47290254..47293439-chr11:47374246..47378968,6	MCF-7	breast:
6	chr11:47196513..47199902-chr11:47376301..47378521,3	K562	blood:
7	chr11:47374545..47377220-chr11:47429148..47430894,2	K562	blood:
8	chr11:47368613..47373799-chr11:47374584..47376990,4	MCF-7	breast:
9	chr11:47182519..47183758-chr11:47376283..47377406,7	MCF-7	breast:
10	chr11:47201336..47204009-chr11:47374499..47376871,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYBPC3	TF binding region
ENSG00000165915	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1057233	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10734557	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742803	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769258	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10769262	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838698	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838699	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838704	0.83[EUR][1000 genomes]
rs10838706	0.87[EUR][1000 genomes]
rs11039195	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11039199	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039200	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039202	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039203	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039212	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039219	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11600581	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11601603	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605672	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11607981	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12146565	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12802273	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12803525	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317164	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053979	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2053980	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2071304	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2084946	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293577	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2293578	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2293580	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2856661	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35496532	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35996350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3740688	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3781624	0.80[EUR][1000 genomes]
rs3781625	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3781626	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4752827	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752987	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752990	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752993	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752994	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4752999	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4992357	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55677087	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55876153	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927797	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56030824	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58965622	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60075622	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6485753	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67116452	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67472071	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7105851	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107726	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs755553	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs755554	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs755555	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7924485	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928163	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928419	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7937331	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7940536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs896815	0.81[EUR][1000 genomes]
rs896816	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs935914	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv3392657	chr11:47376226-47378724	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv3380389	chr11:47376276-47379974	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv3337151	chr11:47376276-47380074	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	esv3439899	chr11:47376276-47381174	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3740686	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs3740686	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs3740686	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs3740686	C1QTNF4	cis	Muscle Skeletal	GTEx
rs3740686	SPI1	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47367800-47377200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47370800-47377000	Weak transcription	K562	blood
3	chr11:47371000-47379800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr11:47372800-47376400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:47373000-47376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:47373800-47376400	Weak transcription	Placenta	Placenta
7	chr11:47373800-47377000	Weak transcription	Fetal Lung	lung
8	chr11:47373800-47377200	Weak transcription	Gastric	stomach
9	chr11:47374000-47376600	Weak transcription	Ovary	ovary
10	chr11:47374200-47377200	Enhancers	Fetal Heart	heart
11	chr11:47374400-47376400	Weak transcription	Right Atrium	heart
12	chr11:47374400-47376400	Weak transcription	Right Ventricle	heart
13	chr11:47374600-47376600	Weak transcription	Pancreas	Pancrea
14	chr11:47374600-47376800	Weak transcription	Spleen	Spleen
15	chr11:47374800-47376600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:47374800-47380400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:47375400-47379600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:47375400-47381000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:47375600-47376400	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr11:47375600-47376600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:47375600-47376600	Enhancers	Left Ventricle	heart
22	chr11:47375600-47377800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:47375600-47379600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:47375600-47380400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:47375600-47380600	Strong transcription	Primary B cells from cord blood	blood
26	chr11:47375600-47381000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:47375800-47376400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr11:47375800-47377400	Active TSS	Brain Cingulate Gyrus	brain
29	chr11:47375800-47377600	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr11:47376000-47376400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr11:47376000-47376400	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr11:47376000-47376400	Enhancers	Brain Substantia Nigra	brain
33	chr11:47376000-47376800	Active TSS	Stomach Smooth Muscle	stomach
34	chr11:47376000-47377200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr11:47376000-47377200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:47376200-47376400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr11:47376200-47376400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr11:47376200-47376400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:47376200-47376400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr11:47376200-47376400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:47376200-47376400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:47376200-47376400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:47376200-47376400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:47376200-47376400	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr11:47376200-47376400	Enhancers	Brain Angular Gyrus	brain
46	chr11:47376200-47376400	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr11:47376200-47376400	Enhancers	Fetal Intestine Large	intestine
48	chr11:47376200-47376400	Enhancers	Fetal Muscle Leg	muscle
49	chr11:47376200-47376400	Enhancers	Fetal Stomach	stomach
50	chr11:47376200-47376400	Enhancers	Rectal Mucosa Donor 29	rectum

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