Variant report

Variant	rs1854779
Chromosome Location	chr1:152880672-152880673
allele	A/G
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	ATF2	chr1:152880275-152880961	GM12878	blood:	n/a	n/a
2	EBF1	chr1:152880501-152880793	GM12878	blood:	n/a	chr1:152880541-152880552
3	NFATC1	chr1:152880381-152880926	GM12878	blood:	n/a	n/a
4	IRF4	chr1:152880481-152880952	GM12878	blood:	n/a	n/a
5	IKZF1	chr1:152880506-152880923	GM12878	blood:	n/a	n/a
6	FOXM1	chr1:152880369-152880973	GM12878	blood:	n/a	n/a
7	PML	chr1:152880301-152881059	GM12878	blood:	n/a	chr1:152880896-152880905
8	RUNX3	chr1:152880280-152881054	GM12878	blood:	n/a	n/a
9	EP300	chr1:152880619-152881140	T-47D	breast:	n/a	n/a
10	EBF1	chr1:152880382-152880852	GM12878	blood:	n/a	chr1:152880541-152880552
11	STAT5A	chr1:152880495-152880912	GM12878	blood:	n/a	chr1:152880524-152880536 chr1:152880638-152880649
12	TBL1XR1	chr1:152880486-152880825	GM12878	blood:	n/a	n/a
13	EP300	chr1:152880653-152881061	T-47D	breast:	n/a	n/a
14	MTA3	chr1:152880188-152881106	GM12878	blood:	n/a	n/a
15	CEBPB	chr1:152880355-152881043	GM12878	blood:	n/a	n/a
16	BCL11A	chr1:152880475-152880870	GM12878	blood:	n/a	chr1:152880838-152880846
17	RELA	chr1:152880450-152880912	GM19193	blood:	n/a	n/a
18	GATA3	chr1:152880643-152881159	T-47D	breast:	n/a	n/a
19	MEF2A	chr1:152880390-152880874	GM12878	blood:	n/a	n/a
20	BCL3	chr1:152880422-152880833	GM12878	blood:	n/a	n/a
21	RUNX3	chr1:152880329-152881080	GM12878	blood:	n/a	n/a
22	EBF1	chr1:152880464-152880874	GM12878	blood:	n/a	chr1:152880541-152880552
23	BATF	chr1:152880414-152881057	GM12878	blood:	n/a	chr1:152880895-152880905
24	BATF	chr1:152880495-152880895	GM12878	blood:	n/a	n/a
25	ATF2	chr1:152880498-152880912	GM12878	blood:	n/a	n/a
26	MTA3	chr1:152880368-152880923	GM12878	blood:	n/a	n/a
27	RELA	chr1:152880414-152880930	GM12878	blood:	n/a	n/a
28	EP300	chr1:152880527-152880886	GM12878	blood:	n/a	n/a
29	BCLAF1	chr1:152880384-152880953	GM12878	blood:	n/a	chr1:152880838-152880846
30	NFIC	chr1:152880325-152880964	GM12878	blood:	n/a	n/a
31	NFIC	chr1:152879957-152881161	GM12878	blood:	n/a	n/a
32	NFATC1	chr1:152880387-152880923	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152879484..152881014-chr1:152889901..152891810,2	MCF-7	breast:

Variant related genes	Relation type
IVL	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11205130	0.80[ASN][1000 genomes]
rs11205131	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs11205132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036697	0.80[ASN][1000 genomes]
rs12239648	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs12239814	0.84[CHD][hapmap]
rs12240158	0.94[EUR][1000 genomes]
rs12406539	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16834746	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs16834751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1974141	0.80[ASN][1000 genomes]
rs2229496	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879485	0.84[CHD][hapmap]
rs34198967	0.93[EUR][1000 genomes]
rs34593101	0.94[EUR][1000 genomes]
rs34599045	0.89[EUR][1000 genomes]
rs35991466	0.93[EUR][1000 genomes]
rs36033488	0.90[EUR][1000 genomes]
rs3820136	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3845340	0.94[EUR][1000 genomes]
rs4523473	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845327	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587711	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7517189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535306	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545413	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545520	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs913996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1854779	S100A7A	cis	parietal	SCAN
rs1854779	LCE1E	cis	parietal	SCAN
rs1854779	SMCP	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152876400-152882600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:152876600-152880800	Enhancers	GM12878-XiMat	blood
3	chr1:152876600-152881800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:152879000-152881000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:152879200-152880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:152879200-152881000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:152879200-152881400	Weak transcription	Esophagus	oesophagus
8	chr1:152879200-152881800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:152879200-152881800	Enhancers	NHEK	skin
10	chr1:152879200-152882200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:152879200-152882400	Enhancers	HMEC	breast
12	chr1:152879400-152881000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:152880600-152880800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:152880600-152880800	Enhancers	NHLF	lung
15	chr1:152880600-152880800	Enhancers	Osteobl	bone
16	chr1:152880600-152881000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:152880600-152881000	Enhancers	NHDF-Ad	bronchial

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