Variant report

Variant	rs17629719
Chromosome Location	chr7:16843983-16843984
allele	G/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	SIN3AK20	chr7:16843518-16845424	MCF-7	breast:	n/a	n/a
2	EP300	chr7:16843296-16844248	A549	lung:	n/a	n/a
3	FOSL2	chr7:16843179-16844185	A549	lung:	n/a	chr7:16843701-16843713 chr7:16843703-16843710 chr7:16843703-16843711
4	POLR2A	chr7:16842327-16844959	MCF-7	breast:	n/a	n/a
5	JUND	chr7:16843350-16844034	T-47D	breast:	n/a	chr7:16843701-16843713 chr7:16843703-16843710 chr7:16843703-16843711
6	CEBPB	chr7:16843361-16844028	A549	lung:	n/a	n/a
7	GATA3	chr7:16843430-16844017	MCF-7	breast:	n/a	n/a
8	TCF12	chr7:16843260-16845410	A549	lung:	n/a	n/a
9	SP1	chr7:16843353-16844202	A549	lung:	n/a	n/a
10	REST	chr7:16843438-16843995	A549	lung:	n/a	n/a
11	GATA3	chr7:16843359-16844162	MCF-7	breast:	n/a	n/a
12	JUND	chr7:16843309-16843984	T-47D	breast:	n/a	chr7:16843701-16843713 chr7:16843703-16843710 chr7:16843703-16843711
13	SP1	chr7:16843403-16844060	A549	lung:	n/a	n/a
14	EP300	chr7:16843352-16844011	T-47D	breast:	n/a	n/a
15	POLR2A	chr7:16843507-16844185	PANC-1	pancreas:	n/a	n/a
16	FOSL2	chr7:16843450-16844000	MCF-7	breast:	n/a	chr7:16843701-16843713 chr7:16843703-16843710 chr7:16843703-16843711
17	FOXA2	chr7:16843406-16844035	A549	lung:	n/a	n/a
18	CEBPB	chr7:16843652-16845006	A549	lung:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
19	EP300	chr7:16843382-16844009	A549	lung:	n/a	n/a
20	GATA3	chr7:16843249-16844206	A549	lung:	n/a	n/a
21	TCF7L2	chr7:16843537-16844139	PANC-1	pancreas:	n/a	n/a
22	MAZ	chr7:16843712-16843992	Hela-S3	cervix:	n/a	n/a
23	FOXA2	chr7:16843398-16844019	A549	lung:	n/a	n/a

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	chr7:16817402..16819269-chr7:16842620..16844289,2	MCF-7	breast:
6	chr7:16835974..16838932-chr7:16840945..16844181,3	MCF-7	breast:
7	chr7:16840761..16845436-chr7:16917964..16923686,10	MCF-7	breast:
8	chr7:16842935..16845400-chr7:16919121..16922153,4	MCF-7	breast:
9	chr7:16842671..16846672-chr7:16872970..16875840,3	MCF-7	breast:

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

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10085446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10224320	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10252977	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10499476	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12665886	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12665957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12666607	0.81[CHB][hapmap]
rs12672294	0.99[ASN][1000 genomes]
rs12672301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12672400	0.99[ASN][1000 genomes]
rs12674385	0.82[ASN][1000 genomes]
rs13229262	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437970	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525744	1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs17136670	0.99[ASN][1000 genomes]
rs17150186	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1917742	0.90[CHB][hapmap]
rs28945075	0.82[ASN][1000 genomes]
rs28945079	0.93[ASN][1000 genomes]
rs3757454	0.99[ASN][1000 genomes]
rs3757455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3807501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3807502	0.99[ASN][1000 genomes]
rs3807503	0.99[ASN][1000 genomes]
rs3817502	0.99[ASN][1000 genomes]
rs3817505	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3817506	0.97[ASN][1000 genomes]
rs3817507	0.97[ASN][1000 genomes]
rs3817508	0.96[ASN][1000 genomes]
rs3817509	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3817510	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3817512	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3823653	0.99[ASN][1000 genomes]
rs55824063	0.98[ASN][1000 genomes]
rs56291875	0.99[ASN][1000 genomes]
rs57997528	0.99[ASN][1000 genomes]
rs61130271	0.98[ASN][1000 genomes]
rs62440423	0.99[ASN][1000 genomes]
rs62440424	0.97[ASN][1000 genomes]
rs62440425	0.99[ASN][1000 genomes]
rs62440459	0.98[ASN][1000 genomes]
rs73073559	0.99[ASN][1000 genomes]
rs73078122	0.82[ASN][1000 genomes]
rs73078127	0.82[ASN][1000 genomes]
rs73078130	0.82[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16835000-16844200	Weak transcription	Psoas Muscle	Psoas
2	chr7:16840600-16844000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr7:16840600-16844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:16840600-16845200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr7:16841200-16844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:16841200-16844800	Active TSS	Colonic Mucosa	Colon
7	chr7:16841200-16845200	Active TSS	Fetal Stomach	stomach
8	chr7:16841400-16844800	Active TSS	Rectal Smooth Muscle	rectum
9	chr7:16841600-16844400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr7:16841600-16844600	Active TSS	Placenta Amnion	Placenta Amnion
11	chr7:16841600-16845400	Active TSS	Fetal Intestine Large	intestine
12	chr7:16842000-16844800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr7:16842000-16845400	Active TSS	Stomach Mucosa	stomach
14	chr7:16842200-16845400	Active TSS	Duodenum Mucosa	Duodenum
15	chr7:16842200-16845400	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr7:16842400-16844600	Active TSS	Gastric	stomach
17	chr7:16843000-16844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:16843000-16844000	Enhancers	Hela-S3	cervix
19	chr7:16843000-16844400	Active TSS	Fetal Intestine Small	intestine
20	chr7:16843200-16844600	Active TSS	Fetal Kidney	kidney
21	chr7:16843600-16844000	Enhancers	HMEC	breast
22	chr7:16843600-16844000	Enhancers	NHEK	skin
23	chr7:16843600-16845000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr7:16843600-16845400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:16843800-16844000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr7:16843800-16844000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr7:16843800-16844600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr7:16843800-16844600	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr7:16843800-16844600	Active TSS	Small Intestine	intestine
30	chr7:16843800-16844600	Active TSS	A549	lung
31	chr7:16843800-16845800	Enhancers	HepG2	liver

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