Variant report

Variant	rs13229262
Chromosome Location	chr7:16842381-16842382
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	POLR2A	chr7:16842327-16844959	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:16683657..16687154-chr7:16840807..16845302,5	MCF-7	breast:
2	chr7:16840668..16842666-chr7:16842784..16844681,2	MCF-7	breast:
3	chr7:16835974..16838932-chr7:16840945..16844181,3	MCF-7	breast:
4	chr7:16840761..16845436-chr7:16917964..16923686,10	MCF-7	breast:

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

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10085446	0.95[ASN][1000 genomes]
rs10224320	0.95[ASN][1000 genomes]
rs10252977	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10499476	0.94[ASN][1000 genomes]
rs12665886	0.99[ASN][1000 genomes]
rs12665957	0.99[ASN][1000 genomes]
rs12672294	0.99[ASN][1000 genomes]
rs12672301	0.99[ASN][1000 genomes]
rs12672400	0.99[ASN][1000 genomes]
rs12674385	0.82[ASN][1000 genomes]
rs13437970	0.94[ASN][1000 genomes]
rs17136670	0.99[ASN][1000 genomes]
rs17150186	0.99[ASN][1000 genomes]
rs17629719	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28945075	0.82[ASN][1000 genomes]
rs28945079	0.93[ASN][1000 genomes]
rs3757454	0.99[ASN][1000 genomes]
rs3757455	0.99[ASN][1000 genomes]
rs3807501	0.99[ASN][1000 genomes]
rs3807502	0.99[ASN][1000 genomes]
rs3807503	0.99[ASN][1000 genomes]
rs3817502	0.99[ASN][1000 genomes]
rs3817505	0.99[ASN][1000 genomes]
rs3817506	0.97[ASN][1000 genomes]
rs3817507	0.97[ASN][1000 genomes]
rs3817508	0.96[ASN][1000 genomes]
rs3817509	0.97[ASN][1000 genomes]
rs3817510	0.99[ASN][1000 genomes]
rs3817512	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16814400-16843800	Weak transcription	Small Intestine	intestine
2	chr7:16823600-16843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:16834000-16842400	Weak transcription	Gastric	stomach
4	chr7:16835000-16844200	Weak transcription	Psoas Muscle	Psoas
5	chr7:16839200-16842600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:16840400-16843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:16840600-16844000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:16840600-16844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:16840600-16845200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr7:16841000-16842400	Transcr. at gene 5' and 3'	A549	lung
11	chr7:16841200-16843600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:16841200-16844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:16841200-16844800	Active TSS	Colonic Mucosa	Colon
14	chr7:16841200-16845200	Active TSS	Fetal Stomach	stomach
15	chr7:16841400-16843600	Weak transcription	HMEC	breast
16	chr7:16841400-16843600	Weak transcription	NHEK	skin
17	chr7:16841400-16844800	Active TSS	Rectal Smooth Muscle	rectum
18	chr7:16841600-16844400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:16841600-16844600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr7:16841600-16845400	Active TSS	Fetal Intestine Large	intestine
21	chr7:16841800-16842400	Active TSS	Fetal Intestine Small	intestine
22	chr7:16842000-16844800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:16842000-16845400	Active TSS	Stomach Mucosa	stomach
24	chr7:16842200-16845400	Active TSS	Duodenum Mucosa	Duodenum
25	chr7:16842200-16845400	Active TSS	Rectal Mucosa Donor 31	rectum

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