Variant report

Variant	rs4886847
Chromosome Location	chr15:77377654-77377655
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	BATF	chr15:77377594-77378131	GM12878	blood:	n/a	n/a
2	PBX3	chr15:77377503-77377973	SK-N-SH	brain:	n/a	n/a
3	EP300	chr15:77377631-77377899	SK-N-SH_RA	brain:	n/a	n/a
4	MAFK	chr15:77377587-77377924	K562	blood:	n/a	n/a
5	CEBPB	chr15:77377581-77377942	Hela-S3	cervix:	n/a	n/a
6	EP300	chr15:77377531-77377930	SK-N-SH_RA	brain:	n/a	n/a
7	TCF12	chr15:77377407-77378051	SK-N-SH	brain:	n/a	n/a
8	CEBPB	chr15:77377574-77377934	K562	blood:	n/a	n/a
9	JUN	chr15:77377576-77377930	K562	blood:	n/a	n/a
10	STAT3	chr15:77377552-77377890	Hela-S3	cervix:	n/a	chr15:77377702-77377713
11	JUND	chr15:77377487-77378049	SK-N-SH	brain:	n/a	chr15:77377741-77377752
12	CUX1	chr15:77377464-77377955	K562	blood:	n/a	n/a
13	RAD21	chr15:77377649-77377843	SK-N-SH_RA	brain:	n/a	n/a
14	PBX3	chr15:77377467-77378017	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr15:77377513-77377899	MCF10A-Er-Src	breast:	n/a	chr15:77377702-77377713
16	MAFF	chr15:77377608-77377922	K562	blood:	n/a	n/a
17	MAX	chr15:77377604-77377926	Hela-S3	cervix:	n/a	n/a
18	USF2	chr15:77377642-77377819	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr15:77377457-77377855	MCF10A-Er-Src	breast:	n/a	chr15:77377702-77377713
20	BACH1	chr15:77377554-77377837	K562	blood:	n/a	n/a
21	CEBPB	chr15:77377574-77377944	IMR90	lung:	n/a	n/a
22	RAD21	chr15:77377611-77377940	Hela-S3	cervix:	n/a	n/a
23	FOS	chr15:77377557-77377933	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT1	chr15:77377350-77377906	Hela-S3	cervix:	n/a	chr15:77377702-77377713
25	RUNX3	chr15:77377577-77378068	GM12878	blood:	n/a	n/a
26	FOSL2	chr15:77377510-77377961	MCF-7	breast:	n/a	n/a
27	ATF1	chr15:77377561-77377886	K562	blood:	n/a	n/a
28	JUND	chr15:77377645-77377845	HepG2	liver:	n/a	chr15:77377741-77377752
29	FOS	chr15:77377565-77377915	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr15:77377519-77377909	MCF10A-Er-Src	breast:	n/a	chr15:77377702-77377713
31	MYC	chr15:77377588-77377876	MCF10A-Er-Src	breast:	n/a	n/a
32	FOSL1	chr15:77377513-77377926	K562	blood:	n/a	n/a
33	STAT3	chr15:77377520-77377899	MCF10A-Er-Src	breast:	n/a	chr15:77377702-77377713
34	TEAD4	chr15:77377550-77377956	K562	blood:	n/a	n/a
35	EP300	chr15:77377636-77377855	K562	blood:	n/a	n/a
36	FOSL2	chr15:77377544-77377977	SK-N-SH	brain:	n/a	n/a
37	FOS	chr15:77377531-77377927	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr15:77377531-77377932	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr15:77377528-77377932	MCF10A-Er-Src	breast:	n/a	chr15:77377702-77377713
40	JUND	chr15:77377559-77377929	K562	blood:	n/a	chr15:77377741-77377752
41	MYC	chr15:77377619-77377863	MCF10A-Er-Src	breast:	n/a	n/a
42	MAX	chr15:77377584-77377910	NB4	blood:	n/a	n/a
43	CEBPB	chr15:77377640-77377817	HepG2	liver:	n/a	n/a
44	CEBPB	chr15:77377606-77377891	A549	lung:	n/a	n/a
45	CEBPB	chr15:77377645-77377928	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77362106..77364633-chr15:77375983..77377903,3	MCF-7	breast:
2	chr15:77377099..77380194-chr15:77383029..77386419,3	K562	blood:

Variant related genes	Relation type
TSPAN3	TF binding region
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11630497	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs11636613	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs11636648	0.91[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs11737	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12148761	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12372961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901188	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12912792	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16968665	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404233	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34443712	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3935339	0.87[JPT][hapmap]
rs4886509	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55645420	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56373017	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62007219	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7166154	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7169831	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7177533	0.81[CHB][hapmap]
rs8032	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs938501	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer 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 target site	23 gene(s)	inside rSNPs	diseases
8	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4886847	PSTPIP1	cis	lymphoblastoid	seeQTL
rs4886847	RP11-797A18.4	cis	Muscle Skeletal	GTEx
rs4886847	RP11-797A18.4	cis	Esophagus Muscularis	GTEx
rs4886847	TSPAN3	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77373600-77380000	Enhancers	Primary B cells from peripheral blood	blood
2	chr15:77376200-77378000	Enhancers	NHDF-Ad	bronchial
3	chr15:77376200-77378400	Enhancers	NHLF	lung
4	chr15:77376200-77378600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:77376400-77377800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:77376400-77377800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:77376400-77377800	Enhancers	GM12878-XiMat	blood
8	chr15:77376400-77378200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:77376600-77378000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:77376600-77378000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr15:77376600-77378000	Enhancers	Osteobl	bone
12	chr15:77376600-77378200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:77376600-77378600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:77376600-77379000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:77376600-77379600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:77376800-77377800	Weak transcription	A549	lung
17	chr15:77376800-77378000	Enhancers	HSMM	muscle
18	chr15:77376800-77378600	Enhancers	HSMMtube	muscle
19	chr15:77376800-77378600	Enhancers	K562	blood
20	chr15:77376800-77395600	Weak transcription	Fetal Intestine Small	intestine
21	chr15:77377000-77377800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:77377000-77377800	Enhancers	NH-A	brain
23	chr15:77377000-77378000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:77377000-77379600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:77377200-77378000	Enhancers	Hela-S3	cervix
26	chr15:77377400-77378000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:77377400-77382600	Weak transcription	Spleen	Spleen
28	chr15:77377600-77377800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:77377600-77377800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr15:77377600-77377800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:77377600-77378000	Weak transcription	Primary B cells from cord blood	blood

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