Variant report

Variant	rs9681394
Chromosome Location	chr3:43256231-43256232
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	chr3:43256085-43256535	MCF-7	breast:	n/a	n/a
2	ESR1	chr3:43256129-43256394	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr3:43256125-43256564	MCF10A-Er-Src	breast:	n/a	chr3:43256342-43256351 chr3:43256340-43256348 chr3:43256343-43256352
4	GATA3	chr3:43256070-43256757	T-47D	breast:	n/a	chr3:43256344-43256353
5	ESR1	chr3:43256096-43256496	T-47D	breast:	n/a	n/a
6	MYC	chr3:43256137-43256417	MCF10A-Er-Src	breast:	n/a	n/a
7	ESR1	chr3:43255981-43256780	T-47D	breast:	n/a	n/a
8	MAX	chr3:43256138-43256872	MCF-7	breast:	n/a	n/a
9	FOS	chr3:43256125-43256527	MCF10A-Er-Src	breast:	n/a	chr3:43256342-43256351 chr3:43256340-43256348 chr3:43256343-43256352
10	KAP1	chr3:43256073-43256539	U2OS	brain:	n/a	chr3:43256341-43256350
11	ESR1	chr3:43256154-43256479	ECC-1	luminal epithelium:	n/a	n/a
12	FOS	chr3:43256126-43256527	MCF10A-Er-Src	breast:	n/a	chr3:43256342-43256351 chr3:43256340-43256348 chr3:43256343-43256352
13	HA-E2F1	chr3:43256038-43256765	MCF-7	breast:	n/a	n/a
14	STAT3	chr3:43256180-43256506	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr3:43256159-43256484	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr3:43256131-43256428	T-47D	breast:	n/a	n/a
17	EP300	chr3:43256068-43256462	MCF-7	breast:	n/a	n/a
18	ESR1	chr3:43256025-43256522	ECC-1	luminal epithelium:	n/a	n/a
19	STAT3	chr3:43256161-43256485	MCF10A-Er-Src	breast:	n/a	n/a
20	GATA3	chr3:43255990-43256766	MCF-7	breast:	n/a	chr3:43256344-43256353
21	FOS	chr3:43256147-43256534	MCF10A-Er-Src	breast:	n/a	chr3:43256342-43256351 chr3:43256340-43256348 chr3:43256343-43256352
22	POLR2A	chr3:43256073-43256435	MCF10A-Er-Src	breast:	n/a	n/a
23	ESR1	chr3:43255997-43256691	T-47D	breast:	n/a	n/a
24	ESR1	chr3:43256042-43256457	T-47D	breast:	n/a	n/a
25	ESR1	chr3:43255962-43256761	T-47D	breast:	n/a	n/a
26	ESR1	chr3:43255969-43256742	T-47D	breast:	n/a	n/a
27	ESR1	chr3:43256142-43256370	ECC-1	luminal epithelium:	n/a	n/a
28	ZNF217	chr3:43256100-43256630	MCF-7	breast:	n/a	n/a
29	EBF1	chr3:43256220-43256544	GM12878	blood:	n/a	chr3:43256378-43256387
30	FOSL2	chr3:43256095-43256512	MCF-7	breast:	n/a	chr3:43256342-43256351 chr3:43256340-43256348 chr3:43256343-43256352

No.	Distal block	Cell Line	Cell type
1	chr3:43233608..43236021-chr3:43256055..43258322,2	MCF-7	breast:
2	chr3:43226507..43227731-chr3:43255831..43257041,6	MCF-7	breast:
3	chr3:43235922..43238512-chr3:43256089..43258366,2	K562	blood:
4	chr3:43254448..43258211-chr3:43258239..43261327,4	K562	blood:
5	chr3:43226566..43227731-chr3:43255831..43257041,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222331	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10865932	0.93[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs12634274	0.81[GIH][hapmap]
rs13095863	0.85[JPT][hapmap]
rs1316296	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316297	0.90[EUR][1000 genomes]
rs1320156	0.90[EUR][1000 genomes]
rs13320571	0.93[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs1588027	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs17075317	1.00[JPT][hapmap]
rs17075335	0.85[JPT][hapmap]
rs17075342	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075378	0.90[EUR][1000 genomes]
rs17075381	0.90[EUR][1000 genomes]
rs17075398	0.90[EUR][1000 genomes]
rs17075597	0.93[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs17075630	0.88[MEX][hapmap]
rs1814902	0.88[EUR][1000 genomes]
rs2372355	0.90[EUR][1000 genomes]
rs4585168	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682675	0.88[EUR][1000 genomes]
rs4682677	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682685	0.86[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs4682872	0.90[EUR][1000 genomes]
rs4682874	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682875	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682876	0.84[EUR][1000 genomes]
rs4682879	0.88[EUR][1000 genomes]
rs4682882	0.82[JPT][hapmap]
rs4683364	0.85[JPT][hapmap]
rs4683366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683367	0.90[EUR][1000 genomes]
rs4683369	0.90[EUR][1000 genomes]
rs6441772	0.82[JPT][hapmap]
rs6781696	0.85[JPT][hapmap]
rs6783741	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs6791641	0.82[JPT][hapmap]
rs6793392	0.85[JPT][hapmap]
rs6800983	0.82[GIH][hapmap]
rs6803929	0.87[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7611123	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621298	1.00[JPT][hapmap]
rs7621511	0.90[EUR][1000 genomes]
rs9311339	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs9683242	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs977911	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs9809273	0.90[EUR][1000 genomes]
rs9820946	0.84[JPT][hapmap]
rs9875582	0.85[JPT][hapmap]
rs9876172	0.88[MEX][hapmap]

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	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs9681394	DYNLRB2	trans	brain	seeQTL
rs9681394	SLC47A2	trans	brain	seeQTL
rs9681394	C14orf45	trans	brain	seeQTL
rs9681394	CAPS	trans	brain	seeQTL
rs9681394	KANK4	trans	brain	seeQTL
rs9681394	FANK1	trans	brain	seeQTL
rs9681394	ZMYND10	trans	brain	seeQTL
rs9681394	CCDC19	trans	brain	seeQTL
rs9681394	C1orf194	trans	brain	seeQTL
rs9681394	IQCG	trans	brain	seeQTL
rs9681394	CAPSL	trans	brain	seeQTL
rs9681394	SPAG6	trans	brain	seeQTL
rs9681394	EFCAB1	trans	brain	seeQTL
rs9681394	CCDC11	trans	brain	seeQTL
rs9681394	FLNC	trans	brain	seeQTL
rs9681394	CCDC37	trans	brain	seeQTL
rs9681394	TCTEX1D1	trans	brain	seeQTL
rs9681394	ST6GALNAC2	trans	brain	seeQTL
rs9681394	ARMC3	trans	brain	seeQTL
rs9681394	TEKT1	trans	brain	seeQTL
rs9681394	SPATA18	trans	brain	seeQTL
rs9681394	FBXO15	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43245000-43258800	Weak transcription	Right Atrium	heart
2	chr3:43247800-43259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:43253200-43262400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:43253400-43259000	Weak transcription	Spleen	Spleen
5	chr3:43253600-43256400	Weak transcription	Pancreas	Pancrea
6	chr3:43253600-43256600	Enhancers	Liver	Liver
7	chr3:43253600-43257400	Weak transcription	Left Ventricle	heart
8	chr3:43254000-43257000	Enhancers	Fetal Intestine Small	intestine
9	chr3:43254000-43257200	Enhancers	HMEC	breast
10	chr3:43254000-43258000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:43254200-43257800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:43254400-43256800	Enhancers	Fetal Intestine Large	intestine
13	chr3:43254400-43257200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:43255200-43256400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:43255200-43256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:43255200-43256400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:43255400-43256400	Weak transcription	Stomach Mucosa	stomach
18	chr3:43255800-43257000	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:43256000-43256600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:43256000-43256600	Enhancers	Fetal Kidney	kidney
21	chr3:43256000-43257000	Flanking Active TSS	NHEK	skin
22	chr3:43256200-43266800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:43256200-43267000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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