Variant report

Variant	rs3934896
Chromosome Location	chr3:46527028-46527029
allele	A/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	FOXM1	chr3:46526297-46527095	ECC-1	luminal epithelium:	n/a	n/a
2	YY1	chr3:46526445-46527178	ECC-1	luminal epithelium:	n/a	chr3:46527059-46527067 chr3:46527048-46527070
3	FOXM1	chr3:46526392-46527055	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr3:46526410-46527140	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr3:46525778-46527060	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr3:46525787-46527086	ECC-1	luminal epithelium:	n/a	chr3:46526330-46526340 chr3:46526059-46526067
7	TCF12	chr3:46525706-46527125	ECC-1	luminal epithelium:	n/a	chr3:46526330-46526340 chr3:46526059-46526067
8	EP300	chr3:46525716-46527159	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr3:46526433-46527092	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr3:46526323-46527096	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr3:46526389-46527195	ECC-1	luminal epithelium:	n/a	n/a
12	E2F6	chr3:46526407-46527073	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFIC	chr3:46525756-46527078	ECC-1	luminal epithelium:	n/a	n/a
14	SPI1	chr3:46526794-46527029	K562	blood:	n/a	chr3:46526920-46526929 chr3:46526917-46526930 chr3:46526831-46526844 chr3:46526921-46526928
15	ZBTB7A	chr3:46526085-46527067	ECC-1	luminal epithelium:	n/a	chr3:46526120-46526128
16	SPI1	chr3:46526836-46527194	HL-60	blood:	n/a	chr3:46527041-46527054 chr3:46526920-46526929 chr3:46526917-46526930 chr3:46526921-46526928
17	MAX	chr3:46525795-46527145	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46526738..46529447-chr3:46598574..46601375,2	K562	blood:

Variant related genes	Relation type
LTF	TF binding region
ENSG00000268324	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10514713	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130093	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130094	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714743	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719033	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489007	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489117	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490169	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496623	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496864	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402151	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037391	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139634	0.80[EUR][1000 genomes]
rs2280407	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28413725	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60986461	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763280	0.80[EUR][1000 genomes]
rs883739	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46511800-46530200	Weak transcription	Right Atrium	heart
2	chr3:46522400-46527400	Enhancers	HSMM	muscle
3	chr3:46522800-46530200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:46522800-46530400	Weak transcription	Gastric	stomach
5	chr3:46523400-46529400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:46524400-46528400	Enhancers	Fetal Intestine Large	intestine
7	chr3:46524600-46528400	Enhancers	Fetal Intestine Small	intestine
8	chr3:46524800-46527600	Enhancers	Fetal Muscle Leg	muscle
9	chr3:46524800-46530400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:46525000-46527400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:46525000-46530600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:46525200-46530000	Weak transcription	NH-A	brain
13	chr3:46525400-46527400	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:46525800-46530400	Weak transcription	Right Ventricle	heart
15	chr3:46526000-46527400	Enhancers	Stomach Mucosa	stomach
16	chr3:46526000-46527400	Enhancers	HSMMtube	muscle
17	chr3:46526200-46527200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:46526200-46527800	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:46526200-46530200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:46526400-46527200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:46526400-46527200	Enhancers	Placenta	Placenta
22	chr3:46526400-46527400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:46526600-46527200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:46526600-46527400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:46526800-46527200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:46526800-46527200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:46526800-46527400	Enhancers	Fetal Lung	lung
28	chr3:46526800-46527400	Enhancers	Pancreas	Pancrea
29	chr3:46526800-46530400	Weak transcription	Spleen	Spleen
30	chr3:46527000-46527200	Flanking Active TSS	HepG2	liver
31	chr3:46527000-46528400	Enhancers	Fetal Kidney	kidney
32	chr3:46527000-46530400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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