Variant report

Variant	rs3807502
Chromosome Location	chr7:16843264-16843265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr7:16843179-16844185	A549	lung:	n/a	chr7:16843701-16843713 chr7:16843703-16843710 chr7:16843703-16843711
2	POLR2A	chr7:16842327-16844959	MCF-7	breast:	n/a	n/a
3	TCF12	chr7:16843260-16845410	A549	lung:	n/a	n/a
4	GATA3	chr7:16842757-16843268	T-47D	breast:	n/a	n/a
5	FOXA1	chr7:16843260-16843932	T-47D	breast:	n/a	n/a
6	GATA3	chr7:16843249-16844206	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10085446	0.96[ASN][1000 genomes]
rs10224320	0.96[ASN][1000 genomes]
rs10252977	0.95[ASN][1000 genomes]
rs10499476	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665886	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665957	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667956	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12672294	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672301	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672400	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12674385	0.83[ASN][1000 genomes]
rs13229262	0.99[ASN][1000 genomes]
rs13437970	0.95[ASN][1000 genomes]
rs1525744	0.88[EUR][1000 genomes]
rs17136670	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17150186	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629719	0.99[ASN][1000 genomes]
rs28945075	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28945079	0.94[ASN][1000 genomes]
rs3757454	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757455	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807501	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807503	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817502	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817505	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817506	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817507	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817508	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817509	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817510	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817512	0.98[ASN][1000 genomes]
rs3823653	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824063	0.99[ASN][1000 genomes]
rs56291875	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57997528	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61130271	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62440423	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440424	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62440425	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440459	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73073559	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73078122	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73078127	0.83[ASN][1000 genomes]
rs73078130	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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:28 , 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	chr7:16835000-16844200	Weak transcription	Psoas Muscle	Psoas
4	chr7:16840400-16843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:16840600-16844000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:16840600-16844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:16840600-16845200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:16841200-16843600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:16841200-16844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:16841200-16844800	Active TSS	Colonic Mucosa	Colon
11	chr7:16841200-16845200	Active TSS	Fetal Stomach	stomach
12	chr7:16841400-16843600	Weak transcription	HMEC	breast
13	chr7:16841400-16843600	Weak transcription	NHEK	skin
14	chr7:16841400-16844800	Active TSS	Rectal Smooth Muscle	rectum
15	chr7:16841600-16844400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:16841600-16844600	Active TSS	Placenta Amnion	Placenta Amnion
17	chr7:16841600-16845400	Active TSS	Fetal Intestine Large	intestine
18	chr7:16842000-16844800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr7:16842000-16845400	Active TSS	Stomach Mucosa	stomach
20	chr7:16842200-16845400	Active TSS	Duodenum Mucosa	Duodenum
21	chr7:16842200-16845400	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr7:16842400-16844600	Active TSS	Gastric	stomach
23	chr7:16843000-16844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:16843000-16844000	Enhancers	Hela-S3	cervix
25	chr7:16843000-16844400	Active TSS	Fetal Intestine Small	intestine
26	chr7:16843200-16843400	Flanking Active TSS	A549	lung
27	chr7:16843200-16843800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr7:16843200-16844600	Active TSS	Fetal Kidney	kidney

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