Variant report

Variant	rs706073
Chromosome Location	chr7:16844681-16844682
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	CEBPB	chr7:16844407-16845255	A549	lung:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
2	SP1	chr7:16844226-16845347	A549	lung:	n/a	n/a
3	SIN3AK20	chr7:16843518-16845424	MCF-7	breast:	n/a	n/a
4	FOSL2	chr7:16844197-16845538	A549	lung:	n/a	chr7:16844237-16844247
5	STAT3	chr7:16844232-16845128	MCF10A-Er-Src	breast:	n/a	n/a
6	TAF1	chr7:16844353-16844902	MCF-7	breast:	n/a	n/a
7	POLR2A	chr7:16844414-16844726	A549	lung:	n/a	n/a
8	TCF7L2	chr7:16844646-16845135	MCF-7	breast:	n/a	n/a
9	CEBPB	chr7:16844245-16844970	Hela-S3	cervix:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
10	SP1	chr7:16844177-16845219	A549	lung:	n/a	n/a
11	MAX	chr7:16844317-16845287	A549	lung:	n/a	n/a
12	FOXA2	chr7:16844340-16845200	A549	lung:	n/a	n/a
13	MYC	chr7:16844457-16845137	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr7:16842327-16844959	MCF-7	breast:	n/a	n/a
15	FOS	chr7:16844445-16845187	MCF10A-Er-Src	breast:	n/a	n/a
16	GATA3	chr7:16844362-16845529	MCF-7	breast:	n/a	n/a
17	SIN3AK20	chr7:16844487-16844861	A549	lung:	n/a	n/a
18	GATA3	chr7:16844260-16845483	A549	lung:	n/a	n/a
19	CEBPB	chr7:16844368-16845187	MCF-7	breast:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
20	POLR2A	chr7:16844486-16844708	ECC-1	luminal epithelium:	n/a	n/a
21	GATA3	chr7:16844345-16845323	MCF-7	breast:	n/a	n/a
22	TCF12	chr7:16843260-16845410	A549	lung:	n/a	n/a
23	EP300	chr7:16844394-16845160	A549	lung:	n/a	n/a
24	FOXM1	chr7:16844492-16845304	MCF-7	breast:	n/a	n/a
25	POLR2A	chr7:16844426-16844693	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr7:16844330-16845110	MCF-7	breast:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
27	GATA3	chr7:16844537-16845151	MCF-7	breast:	n/a	n/a
28	JUND	chr7:16844386-16845262	T-47D	breast:	n/a	n/a
29	POLR2A	chr7:16844287-16844871	PANC-1	pancreas:	n/a	n/a
30	SIN3AK20	chr7:16844300-16845218	MCF-7	breast:	n/a	n/a
31	TAF1	chr7:16844224-16844763	A549	lung:	n/a	n/a
32	TCF12	chr7:16844445-16845188	MCF-7	breast:	n/a	n/a
33	POLR2A	chr7:16844383-16844849	ProgFib	skin:	n/a	n/a
34	EP300	chr7:16844425-16845416	A549	lung:	n/a	chr7:16845192-16845206 chr7:16845191-16845205 chr7:16845193-16845207 chr7:16845194-16845208
35	CEBPB	chr7:16844392-16845062	A549	lung:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
36	GATA3	chr7:16844426-16845147	T-47D	breast:	n/a	n/a
37	POLR2A	chr7:16844485-16844728	A549	lung:	n/a	n/a
38	FOS	chr7:16844439-16845191	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr7:16844271-16844914	MCF-7	breast:	n/a	n/a
40	POLR2A	chr7:16844435-16845128	MCF10A-Er-Src	breast:	n/a	n/a
41	HDAC2	chr7:16844407-16845246	MCF-7	breast:	n/a	chr7:16845196-16845210 chr7:16845192-16845206 chr7:16845190-16845204 chr7:16845193-16845207 chr7:16845194-16845208 chr7:16845131-16845145 chr7:16845191-16845205
42	STAT3	chr7:16844241-16845248	MCF10A-Er-Src	breast:	n/a	n/a
43	ZNF217	chr7:16844482-16845180	MCF-7	breast:	n/a	n/a
44	EP300	chr7:16844369-16845072	T-47D	breast:	n/a	n/a
45	GATA3	chr7:16844412-16845183	T-47D	breast:	n/a	n/a
46	NFIC	chr7:16844346-16845187	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr7:16844432-16844731	A549	lung:	n/a	n/a
48	ESR1	chr7:16844667-16845079	T-47D	breast:	n/a	n/a
49	FOSL2	chr7:16844655-16845231	MCF-7	breast:	n/a	n/a
50	CEBPB	chr7:16843652-16845006	A549	lung:	n/a	chr7:16844780-16844791 chr7:16844778-16844791

No.	Distal block	Cell Line	Cell type
1	chr7:16792720..16796708-chr7:16843218..16846000,6	MCF-7	breast:
2	chr7:16683657..16687154-chr7:16840807..16845302,5	MCF-7	breast:
3	chr7:16840668..16842666-chr7:16842784..16844681,2	MCF-7	breast:
4	chr7:16843625..16845723-chr7:16926394..16928363,2	MCF-7	breast:
5	chr7:16840761..16845436-chr7:16917964..16923686,10	MCF-7	breast:
6	chr7:16842935..16845400-chr7:16919121..16922153,4	MCF-7	breast:
7	chr7:16842671..16846672-chr7:16872970..16875840,3	MCF-7	breast:

Variant related genes	Relation type
AGR2	TF binding region
ENSG00000106541	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000227965	Chromatin interaction
ENSG00000106537	Chromatin interaction
ENSG00000106524	Chromatin interaction
ENSG00000173467	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10231868	0.93[EUR][1000 genomes]
rs10245233	0.93[EUR][1000 genomes]
rs10268768	0.93[EUR][1000 genomes]
rs10275420	0.91[EUR][1000 genomes]
rs10279569	0.92[EUR][1000 genomes]
rs12668575	0.86[TSI][hapmap]
rs13229674	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1404966	0.86[TSI][hapmap]
rs1459563	0.81[CEU][hapmap]
rs1474414	0.92[EUR][1000 genomes]
rs1474415	0.90[EUR][1000 genomes]
rs17136685	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17136690	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17136694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2389703	0.92[EUR][1000 genomes]
rs6959114	0.86[TSI][hapmap]
rs6966839	0.90[TSI][hapmap]
rs706075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706079	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706080	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[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	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs706073	AGR2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16840600-16845200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:16841200-16844800	Active TSS	Colonic Mucosa	Colon
3	chr7:16841200-16845200	Active TSS	Fetal Stomach	stomach
4	chr7:16841400-16844800	Active TSS	Rectal Smooth Muscle	rectum
5	chr7:16841600-16845400	Active TSS	Fetal Intestine Large	intestine
6	chr7:16842000-16844800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr7:16842000-16845400	Active TSS	Stomach Mucosa	stomach
8	chr7:16842200-16845400	Active TSS	Duodenum Mucosa	Duodenum
9	chr7:16842200-16845400	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr7:16843600-16845000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:16843600-16845400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:16843800-16845800	Enhancers	HepG2	liver
13	chr7:16844000-16844800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:16844000-16844800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr7:16844000-16844800	Flanking Active TSS	NHEK	skin
16	chr7:16844000-16845000	Flanking Active TSS	Hela-S3	cervix
17	chr7:16844000-16845000	Flanking Active TSS	HMEC	breast
18	chr7:16844200-16844800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:16844200-16845000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:16844400-16844800	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr7:16844400-16845400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:16844600-16845000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:16844600-16845200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr7:16844600-16845600	Flanking Active TSS	A549	lung
25	chr7:16844600-16854800	Weak transcription	Small Intestine	intestine

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