Variant report

Variant	rs11917839
Chromosome Location	chr3:112470970-112470971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr3:112470298-112471455	ECC-1	luminal epithelium:	n/a	n/a
2	NR3C1	chr3:112470875-112471321	A549	lung:	n/a	n/a
3	FOXA1	chr3:112470969-112471327	ECC-1	luminal epithelium:	n/a	n/a
4	SP1	chr3:112470835-112471399	A549	lung:	n/a	n/a
5	EP300	chr3:112470236-112471414	ECC-1	luminal epithelium:	n/a	chr3:112470312-112470326 chr3:112470310-112470324
6	ESR1	chr3:112470876-112471368	ECC-1	luminal epithelium:	n/a	n/a
7	ESR1	chr3:112470912-112471353	ECC-1	luminal epithelium:	n/a	n/a
8	JUND	chr3:112470862-112471417	A549	lung:	n/a	n/a
9	TCF12	chr3:112470248-112471506	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr3:112470572-112471530	A549	lung:	n/a	n/a
11	CCNT2	chr3:112470724-112470998	K562	blood:	n/a	n/a
12	NFIC	chr3:112470918-112471391	ECC-1	luminal epithelium:	n/a	n/a
13	KAP1	chr3:112470385-112471475	HEK293	kidney:	n/a	n/a
14	NFIC	chr3:112470880-112471374	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr3:112470844-112471470	A549	lung:	n/a	n/a
16	ESR1	chr3:112470965-112471400	ECC-1	luminal epithelium:	n/a	n/a
17	ESR1	chr3:112470929-112471368	ECC-1	luminal epithelium:	n/a	n/a
18	SP1	chr3:112470711-112471406	A549	lung:	n/a	n/a
19	FOSL2	chr3:112470403-112471416	A549	lung:	n/a	n/a
20	TCF12	chr3:112470909-112471505	ECC-1	luminal epithelium:	n/a	n/a
21	FOXA2	chr3:112470735-112471383	A549	lung:	n/a	n/a
22	TCF7L2	chr3:112470427-112471225	HEK293	kidney:	n/a	n/a
23	FOXA2	chr3:112470860-112471495	A549	lung:	n/a	n/a
24	FOXA1	chr3:112470953-112471267	ECC-1	luminal epithelium:	n/a	n/a
25	TCF12	chr3:112470249-112471541	A549	lung:	n/a	n/a
26	ESR1	chr3:112470872-112471373	ECC-1	luminal epithelium:	n/a	n/a
27	TEAD4	chr3:112470940-112471416	ECC-1	luminal epithelium:	n/a	n/a
28	KAP1	chr3:112470441-112471307	U2OS	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112465788..112467955-chr3:112468785..112471247,2	K562	blood:
2	chr3:112461762..112464702-chr3:112469113..112471587,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240893	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12489081	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496168	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35106456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912626	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59902023	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6781277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781391	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781609	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781823	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805944	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806013	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806104	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946393	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646744	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646996	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820548	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs864238	1.00[YRI][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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112468000-112472000	Enhancers	A549	lung
2	chr3:112468000-112478200	Weak transcription	K562	blood
3	chr3:112468000-112488200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:112468200-112471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112469000-112472000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:112469200-112471800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:112470000-112472600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:112470400-112471000	Enhancers	Fetal Intestine Small	intestine
9	chr3:112470400-112471200	Enhancers	Fetal Intestine Large	intestine
10	chr3:112470400-112471400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr3:112470600-112471200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:112470600-112471200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:112470600-112471200	Enhancers	Colon Smooth Muscle	Colon
14	chr3:112470600-112471200	Enhancers	HSMM	muscle
15	chr3:112470600-112471400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:112470600-112472800	Enhancers	Stomach Mucosa	stomach
17	chr3:112470800-112471200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:112470800-112471200	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:112470800-112471200	Enhancers	NHDF-Ad	bronchial
20	chr3:112470800-112471400	Enhancers	Fetal Kidney	kidney
21	chr3:112470800-112471800	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:112470800-112472000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:112470800-112472200	Enhancers	Esophagus	oesophagus

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