Variant report

Variant	rs2250145
Chromosome Location	chr5:147286054-147286055
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	E2F4	chr5:147286029-147286246	MCF10A-Er-Src	breast:	n/a	chr5:147286143-147286152
2	CEBPB	chr5:147286017-147286314	A549	lung:	n/a	n/a
3	STAT3	chr5:147286012-147286330	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr5:147285969-147286330	MCF10A-Er-Src	breast:	n/a	n/a
5	RFX5	chr5:147285907-147286305	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:147285925-147286183	Hela-S3	cervix:	n/a	n/a
7	MAX	chr5:147285903-147286548	Hela-S3	cervix:	n/a	n/a
8	FOS	chr5:147285978-147286341	MCF10A-Er-Src	breast:	n/a	chr5:147286144-147286153
9	JUN	chr5:147286009-147286302	HepG2	liver:	n/a	chr5:147286144-147286153 chr5:147286143-147286156
10	USF2	chr5:147286002-147286149	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr5:147285972-147286309	Hela-S3	cervix:	n/a	n/a
12	FOS	chr5:147285949-147286344	MCF10A-Er-Src	breast:	n/a	chr5:147286144-147286153
13	CEBPB	chr5:147285923-147286385	Hela-S3	cervix:	n/a	n/a
14	MYC	chr5:147285929-147286593	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr5:147285991-147286350	MCF10A-Er-Src	breast:	n/a	chr5:147286144-147286153
16	GATA3	chr5:147285782-147286488	SK-N-SH	brain:	n/a	chr5:147286416-147286424
17	EP300	chr5:147285946-147286376	Hela-S3	cervix:	n/a	n/a
18	TBP	chr5:147285984-147286319	Hela-S3	cervix:	n/a	n/a
19	RCOR1	chr5:147285971-147286486	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:147285900-147286256	SK-N-SH	brain:	n/a	n/a
21	JUND	chr5:147285961-147286324	HepG2	liver:	n/a	chr5:147286144-147286153
22	GATA3	chr5:147285850-147286242	T-47D	breast:	n/a	n/a
23	ARID3A	chr5:147286007-147286246	HepG2	liver:	n/a	n/a
24	CEBPB	chr5:147285982-147286371	IMR90	lung:	n/a	n/a
25	CEBPB	chr5:147285944-147286326	MCF-7	breast:	n/a	n/a
26	CEBPB	chr5:147285959-147286295	MCF-7	breast:	n/a	n/a
27	JUN	chr5:147285957-147286401	Hela-S3	cervix:	n/a	chr5:147286144-147286153 chr5:147286143-147286156
28	FOS	chr5:147285967-147286336	MCF10A-Er-Src	breast:	n/a	chr5:147286144-147286153
29	MYC	chr5:147285939-147286614	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr5:147285911-147286392	MCF10A-Er-Src	breast:	n/a	n/a
31	CHD2	chr5:147285886-147286280	Hela-S3	cervix:	n/a	n/a
32	GATA3	chr5:147285757-147286485	SK-N-SH	brain:	n/a	chr5:147286416-147286424
33	CEBPB	chr5:147285984-147286351	HepG2	liver:	n/a	n/a
34	JUND	chr5:147285975-147286476	Hela-S3	cervix:	n/a	chr5:147286144-147286153

Variant related genes	Relation type
C5orf46	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1010764	0.80[LWK][hapmap];0.80[YRI][hapmap]
rs1153085	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153088	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv520730	chr5:147285713-147286054	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250145	SCGB3A2	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147273400-147289000	Weak transcription	Left Ventricle	heart
2	chr5:147283400-147286800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147283600-147286800	Enhancers	HMEC	breast
4	chr5:147284000-147286200	Active TSS	Aorta	Aorta
5	chr5:147284000-147286400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:147284200-147291000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:147285000-147286200	Active TSS	Right Ventricle	heart
8	chr5:147285000-147286800	Enhancers	Fetal Heart	heart
9	chr5:147285400-147286800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:147285600-147286800	Enhancers	Hela-S3	cervix
11	chr5:147285800-147286200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:147285800-147286200	Flanking Active TSS	NH-A	brain
13	chr5:147285800-147286200	Flanking Active TSS	Osteobl	bone
14	chr5:147285800-147286600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:147285800-147286600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:147285800-147286600	Enhancers	HSMM	muscle
17	chr5:147285800-147286800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:147285800-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:147285800-147286800	Enhancers	Placenta	Placenta
20	chr5:147286000-147286200	Enhancers	Right Atrium	heart
21	chr5:147286000-147286200	Enhancers	Stomach Mucosa	stomach
22	chr5:147286000-147286200	Flanking Active TSS	HSMMtube	muscle
23	chr5:147286000-147286600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:147286000-147286600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:147286000-147286600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:147286000-147286600	Enhancers	Gastric	stomach
27	chr5:147286000-147286600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr5:147286000-147286600	Flanking Active TSS	NHEK	skin
29	chr5:147286000-147286800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:147286000-147286800	Enhancers	Pancreas	Pancrea

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