Variant report

Variant	rs3817507
Chromosome Location	chr7:16844323-16844324
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	SP1	chr7:16844226-16845347	A549	lung:	n/a	n/a
2	SIN3AK20	chr7:16843518-16845424	MCF-7	breast:	n/a	n/a
3	FOSL2	chr7:16844197-16845538	A549	lung:	n/a	chr7:16844237-16844247
4	STAT3	chr7:16844232-16845128	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr7:16844245-16844970	Hela-S3	cervix:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
6	SP1	chr7:16844177-16845219	A549	lung:	n/a	n/a
7	MAX	chr7:16844317-16845287	A549	lung:	n/a	n/a
8	POLR2A	chr7:16842327-16844959	MCF-7	breast:	n/a	n/a
9	GATA3	chr7:16844260-16845483	A549	lung:	n/a	n/a
10	TCF12	chr7:16843260-16845410	A549	lung:	n/a	n/a
11	POLR2A	chr7:16844287-16844871	PANC-1	pancreas:	n/a	n/a
12	SIN3AK20	chr7:16844300-16845218	MCF-7	breast:	n/a	n/a
13	TAF1	chr7:16844224-16844763	A549	lung:	n/a	n/a
14	POLR2A	chr7:16844271-16844914	MCF-7	breast:	n/a	n/a
15	STAT3	chr7:16844241-16845248	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr7:16843652-16845006	A549	lung:	n/a	chr7:16844780-16844791 chr7:16844778-16844791
17	FOS	chr7:16844297-16845202	MCF10A-Er-Src	breast:	n/a	n/a
18	NFIC	chr7:16844234-16845267	ECC-1	luminal epithelium:	n/a	n/a
19	JUND	chr7:16844309-16845146	T-47D	breast:	n/a	n/a
20	POLR2A	chr7:16844169-16844813	PANC-1	pancreas:	n/a	n/a
21	REST	chr7:16844226-16845081	A549	lung:	n/a	n/a
22	POLR2A	chr7:16844287-16844912	MCF-7	breast:	n/a	n/a
23	STAT3	chr7:16844256-16845260	MCF10A-Er-Src	breast:	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	chr7:16840761..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
ENSG00000106524	Chromatin interaction
ENSG00000106537	Chromatin interaction
ENSG00000227965	Chromatin interaction
ENSG00000173467	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000106541	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	0.93[ASN][1000 genomes]
rs10224320	0.93[ASN][1000 genomes]
rs10252977	0.92[ASN][1000 genomes]
rs10499476	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12665886	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665957	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667956	0.85[EUR][1000 genomes]
rs12672294	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12672301	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12672400	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12674385	0.81[ASN][1000 genomes]
rs13229262	0.97[ASN][1000 genomes]
rs13437970	0.92[ASN][1000 genomes]
rs1525744	0.86[EUR][1000 genomes]
rs17136670	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17150186	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17629719	0.97[ASN][1000 genomes]
rs28945075	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28945079	0.91[ASN][1000 genomes]
rs3757454	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757455	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807501	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807502	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807503	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817502	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817509	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817512	0.96[ASN][1000 genomes]
rs3823653	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55824063	0.97[ASN][1000 genomes]
rs56291875	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57997528	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61130271	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62440423	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62440424	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62440425	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62440459	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73073559	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73078122	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73078127	0.81[ASN][1000 genomes]
rs73078130	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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	chr7:16840600-16845200	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	chr7:16841600-16844400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:16841600-16844600	Active TSS	Placenta Amnion	Placenta Amnion
7	chr7:16841600-16845400	Active TSS	Fetal Intestine Large	intestine
8	chr7:16842000-16844800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr7:16842000-16845400	Active TSS	Stomach Mucosa	stomach
10	chr7:16842200-16845400	Active TSS	Duodenum Mucosa	Duodenum
11	chr7:16842200-16845400	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr7:16842400-16844600	Active TSS	Gastric	stomach
13	chr7:16843000-16844400	Active TSS	Fetal Intestine Small	intestine
14	chr7:16843200-16844600	Active TSS	Fetal Kidney	kidney
15	chr7:16843600-16845000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:16843600-16845400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:16843800-16844600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr7:16843800-16844600	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr7:16843800-16844600	Active TSS	Small Intestine	intestine
20	chr7:16843800-16844600	Active TSS	A549	lung
21	chr7:16843800-16845800	Enhancers	HepG2	liver
22	chr7:16844000-16844600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr7:16844000-16844800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:16844000-16844800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr7:16844000-16844800	Flanking Active TSS	NHEK	skin
26	chr7:16844000-16845000	Flanking Active TSS	Hela-S3	cervix
27	chr7:16844000-16845000	Flanking Active TSS	HMEC	breast
28	chr7:16844200-16844400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr7:16844200-16844600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:16844200-16844800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:16844200-16845000	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links