Variant report

Variant	rs12099041
Chromosome Location	chr11:66232773-66232774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr11:66232763-66233528	GM12878	blood:	n/a	chr11:66233117-66233128 chr11:66233118-66233127 chr11:66233116-66233129
2	MYC	chr11:66232721-66233092	NB4	blood:	n/a	n/a
3	CTCF	chr11:66232740-66232890	GM12878	blood:	n/a	chr11:66232850-66232859

No.	Distal block	Cell Line	Cell type
1	chr11:66232704..66235668-chr11:66609805..66612233,2	MCF-7	breast:
2	chr11:66204104..66208501-chr11:66232741..66235835,4	K562	blood:
3	chr11:66112568..66115991-chr11:66232682..66235735,3	K562	blood:
4	chr11:66204033..66208144-chr11:66232603..66235665,3	K562	blood:
5	chr11:66217732..66219422-chr11:66230658..66233327,2	K562	blood:

Variant related genes	Relation type
PELI3	TF binding region
ENSG00000173653	Chromatin interaction
ENSG00000174684	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000255468	Chromatin interaction
ENSG00000174744	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10501397	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896124	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896125	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10896129	0.90[EUR][1000 genomes]
rs11227495	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227497	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227498	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227499	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227500	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227501	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227502	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227503	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227509	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227510	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227511	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227512	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227514	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227515	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227522	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11227523	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227525	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11227527	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227534	0.90[EUR][1000 genomes]
rs11550299	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11821155	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11822028	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11822099	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11824771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12221821	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12223479	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12272545	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17065	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17147644	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17495838	0.89[EUR][1000 genomes]
rs17496250	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17496586	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17580784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2075792	0.90[EUR][1000 genomes]
rs2276406	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2277302	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279864	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279865	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298806	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305532	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305533	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305534	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305535	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28414721	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3179961	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35733139	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737525	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3741360	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816492	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3819247	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825065	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3867131	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3892818	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4542420	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4576	0.90[EUR][1000 genomes]
rs4630309	0.90[EUR][1000 genomes]
rs4930182	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930183	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930377	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4930378	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930379	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930380	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56144989	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57045447	0.90[EUR][1000 genomes]
rs57207756	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57288351	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57596493	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57634456	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57691879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57724777	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59829960	0.90[EUR][1000 genomes]
rs59982644	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60358007	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60645853	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61561111	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61582507	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104378	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7116921	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116940	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123176	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7928882	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939759	0.90[EUR][1000 genomes]
rs7943327	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950407	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950790	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv897786	chr11:66203025-66244015	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12099041	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12099041	DPP3	cis	Thyroid	GTEx
rs12099041	CTD-3074O7.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66219800-66233800	Weak transcription	Aorta	Aorta
2	chr11:66227000-66233200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:66227200-66233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:66229200-66232800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:66229800-66233400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:66230000-66233400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr11:66232200-66233200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr11:66232200-66233400	Enhancers	Primary B cells from cord blood	blood
9	chr11:66232200-66233400	Enhancers	Primary B cells from peripheral blood	blood
10	chr11:66232200-66233400	Enhancers	Fetal Thymus	thymus
11	chr11:66232200-66233600	Enhancers	Fetal Muscle Leg	muscle
12	chr11:66232400-66232800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:66232400-66232800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr11:66232400-66232800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:66232400-66233000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:66232400-66233000	Enhancers	GM12878-XiMat	blood
17	chr11:66232400-66233200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr11:66232400-66233200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:66232400-66233400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:66232400-66233400	Enhancers	Primary hematopoietic stem cells	blood
21	chr11:66232400-66233400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:66232400-66233400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:66232400-66233400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr11:66232400-66233600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:66232400-66233600	Enhancers	Fetal Muscle Trunk	muscle
26	chr11:66232400-66233600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr11:66232400-66233800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:66232400-66233800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:66232400-66234000	Enhancers	HSMMtube	muscle
30	chr11:66232600-66232800	Active TSS	Brain Germinal Matrix	brain
31	chr11:66232600-66233000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr11:66232600-66233000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:66232600-66233200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:66232600-66233400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr11:66232600-66233400	Bivalent Enhancer	HepG2	liver
36	chr11:66232600-66233600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:66232600-66233600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:66232600-66233600	Enhancers	Fetal Heart	heart
39	chr11:66232600-66233600	Enhancers	Skeletal Muscle Female	skeletal muscle

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