Variant report

Variant	rs3846722
Chromosome Location	chr5:112825424-112825425
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	EP300	chr5:112825014-112825435	SK-N-SH_RA	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
2	FOS	chr5:112824950-112825432	HUVEC	blood vessel:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
3	EBF1	chr5:112825237-112825492	GM12878	blood:	n/a	n/a
4	STAT3	chr5:112825092-112825505	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
5	POLR2A	chr5:112824960-112825488	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr5:112825017-112825580	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr5:112825014-112825560	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
8	JUND	chr5:112824784-112825647	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
9	MYC	chr5:112824005-112825442	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
10	SP1	chr5:112824888-112825620	HCT-116	colon:	n/a	n/a
11	MAX	chr5:112824869-112825529	SK-N-SH	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
12	FOS	chr5:112824953-112825510	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
13	CBX3	chr5:112824784-112825698	HCT-116	colon:	n/a	n/a
14	FOSL1	chr5:112824934-112825697	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
15	STAT3	chr5:112824981-112825433	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
16	CTCF	chr5:112825300-112825450	AG04449	skin:	n/a	n/a
17	MYC	chr5:112825027-112825428	NB4	blood:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
18	FOSL2	chr5:112824948-112825456	A549	lung:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
19	GATA3	chr5:112824770-112825588	SK-N-SH	brain:	n/a	chr5:112825225-112825234
20	CEBPB	chr5:112824567-112825739	HCT-116	colon:	n/a	n/a
21	MAX	chr5:112823020-112825593	HCT-116	colon:	n/a	chr5:112823284-112823295 chr5:112825226-112825235 chr5:112825227-112825236
22	TCF12	chr5:112824885-112825690	SK-N-SH	brain:	n/a	n/a
23	EBF1	chr5:112825245-112825552	GM12878	blood:	n/a	n/a
24	PBX3	chr5:112824919-112825529	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr5:112824917-112825533	SK-N-SH	brain:	n/a	n/a
26	JUND	chr5:112823928-112825693	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
27	SP1	chr5:112824749-112825647	HCT-116	colon:	n/a	n/a
28	JUND	chr5:112824881-112825591	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
29	JUND	chr5:112824912-112825620	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
30	YY1	chr5:112824957-112825444	SK-N-SH	brain:	n/a	n/a
31	TEAD4	chr5:112825042-112825523	ECC-1	luminal epithelium:	n/a	n/a
32	JUND	chr5:112823904-112825645	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
33	RUNX3	chr5:112824932-112825444	GM12878	blood:	n/a	chr5:112825212-112825221 chr5:112825212-112825221
34	MAX	chr5:112824877-112825545	SK-N-SH	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
35	POLR2A	chr5:112823537-112825448	IMR90	lung:	n/a	n/a
36	FOS	chr5:112824962-112825506	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
37	GATA3	chr5:112824853-112825613	SK-N-SH	brain:	n/a	chr5:112825225-112825234
38	FOSL1	chr5:112823968-112825681	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
39	TEAD4	chr5:112824954-112825542	SK-N-SH	brain:	n/a	n/a
40	E2F4	chr5:112824987-112825484	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr5:112824914-112825510	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
42	TCF12	chr5:112824829-112825649	SK-N-SH	brain:	n/a	n/a
43	CEBPB	chr5:112825010-112825691	IMR90	lung:	n/a	n/a
44	EP300	chr5:112824871-112825617	SK-N-SH	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
45	POLR2A	chr5:112824903-112825482	HCT-116	colon:	n/a	n/a
46	FOSL2	chr5:112824929-112825456	MCF-7	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
47	FOSL2	chr5:112824913-112825565	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
48	KAP1	chr5:112823836-112825464	HEK293	kidney:	n/a	chr5:112825228-112825237
49	FOS	chr5:112825024-112825495	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
50	NFIC	chr5:112824732-112825597	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112823438..112825437-chr5:112848716..112850682,3	MCF-7	breast:
2	chr5:112823064..112825616-chr5:112827873..112829693,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region
RNU4ATAC13P	TF binding region
ENSG00000251741	Chromatin interaction
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap]
rs10071816	0.94[CEU][hapmap]
rs10079895	0.94[CEU][hapmap]
rs10079973	0.94[CEU][hapmap]
rs10080096	0.89[CEU][hapmap]
rs10428666	0.85[JPT][hapmap]
rs10477497	0.88[CEU][hapmap]
rs10478127	0.94[CEU][hapmap]
rs10900685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1116547	0.88[JPT][hapmap]
rs11241201	0.88[JPT][hapmap]
rs11241206	0.88[JPT][hapmap]
rs11241214	0.94[CEU][hapmap]
rs11241215	0.88[CEU][hapmap]
rs11738075	0.88[JPT][hapmap]
rs11738215	0.88[JPT][hapmap]
rs11741963	0.82[ASN][1000 genomes]
rs11747924	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11748145	0.89[EUR][1000 genomes]
rs11748794	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap]
rs11750945	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11956399	0.94[CEU][hapmap]
rs12186798	0.94[CEU][hapmap]
rs12514091	0.88[JPT][hapmap]
rs12516418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12519323	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12519818	0.89[ASN][1000 genomes]
rs12523255	0.85[JPT][hapmap]
rs12660001	0.94[CEU][hapmap]
rs1443683	0.86[JPT][hapmap]
rs17135597	0.86[JPT][hapmap]
rs17135608	0.86[JPT][hapmap]
rs17135616	0.88[JPT][hapmap];0.88[YRI][hapmap]
rs17135630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs17135753	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17135754	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1833678	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850410	0.88[JPT][hapmap]
rs2042222	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2068923	0.88[JPT][hapmap]
rs2288449	0.94[CEU][hapmap]
rs2416281	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763140	0.94[CEU][hapmap]
rs3815911	0.94[CEU][hapmap]
rs3846721	0.88[JPT][hapmap];0.88[YRI][hapmap]
rs3936061	0.94[CEU][hapmap]
rs4122546	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4334877	0.88[CEU][hapmap]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705814	0.88[JPT][hapmap]
rs4705817	0.86[JPT][hapmap]
rs4705819	0.85[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57077871	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6594734	0.94[CEU][hapmap]
rs66490974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66497221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66502937	0.89[ASN][1000 genomes]
rs66583752	0.89[ASN][1000 genomes]
rs66644309	0.82[ASN][1000 genomes]
rs67020702	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67103739	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67268709	0.89[ASN][1000 genomes]
rs67723806	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6859688	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6861786	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6864369	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6864528	0.88[JPT][hapmap]
rs6877432	0.89[CEU][hapmap]
rs6877524	0.88[JPT][hapmap]
rs6878001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs6882900	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap]
rs6883441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6886628	0.94[CEU][hapmap]
rs6889574	0.94[CEU][hapmap]
rs6896469	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6896501	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898425	0.82[CEU][hapmap]
rs72792179	0.89[ASN][1000 genomes]
rs72794121	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72805465	0.84[EUR][1000 genomes]
rs73241779	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73242809	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73247445	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7349799	0.87[CEU][hapmap]
rs7702833	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706958	0.94[CEU][hapmap]
rs7707443	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap]
rs7711367	0.94[CEU][hapmap]
rs7717000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7729433	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7737023	0.94[CEU][hapmap]
rs919304	0.94[CEU][hapmap]
rs9326893	0.94[CEU][hapmap]
rs957777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3846722	YTHDC2	cis	multi-tissue	Pritchard
rs3846722	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112823400-112825600	Active TSS	Brain Anterior Caudate	brain
2	chr5:112823800-112825600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:112823800-112826800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr5:112824200-112825600	Flanking Active TSS	NH-A	brain
5	chr5:112824400-112825600	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr5:112824400-112825800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:112824400-112825800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr5:112824600-112825600	Enhancers	Esophagus	oesophagus
9	chr5:112824600-112825600	Enhancers	Hela-S3	cervix
10	chr5:112824600-112825800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr5:112824600-112826000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:112824600-112826000	Enhancers	Dnd41	blood
13	chr5:112824800-112825600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:112824800-112825600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:112824800-112825600	Enhancers	HUVEC	blood vessel
16	chr5:112824800-112825800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:112824800-112826000	Enhancers	NHLF	lung
18	chr5:112825000-112825600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:112825000-112825800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:112825000-112825800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:112825000-112826000	Enhancers	HMEC	breast
22	chr5:112825000-112826000	Enhancers	NHEK	skin
23	chr5:112825200-112825600	Enhancers	Aorta	Aorta
24	chr5:112825200-112825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:112825200-112825800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr5:112825200-112825800	Enhancers	NHDF-Ad	bronchial
27	chr5:112825200-112825800	Enhancers	Osteobl	bone
28	chr5:112825400-112825600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:112825400-112825600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:112825400-112825600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:112825400-112825600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:112825400-112825600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr5:112825400-112825600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:112825400-112825600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:112825400-112825600	Flanking Active TSS	HSMM	muscle
36	chr5:112825400-112825800	Flanking Active TSS	HSMMtube	muscle
37	chr5:112825400-112827600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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