Variant report

Variant	rs17028821
Chromosome Location	chr4:100244987-100244988
allele	A/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	FOS	chr4:100244853-100245186	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:100244948-100245135	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr4:100244830-100245030	MCF10A-Er-Src	breast:	n/a	chr4:100244910-100244930 chr4:100244901-100244924
4	FOS	chr4:100244855-100245184	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr4:100244778-100245254	MCF10A-Er-Src	breast:	n/a	chr4:100245151-100245160
6	STAT3	chr4:100244559-100245105	MCF10A-Er-Src	breast:	n/a	chr4:100244910-100244930 chr4:100244901-100244924
7	POLR2A	chr4:100244915-100245334	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr4:100244960-100245110	AG09319	gingival:	n/a	n/a
9	MYC	chr4:100244844-100245202	MCF10A-Er-Src	breast:	n/a	chr4:100245151-100245160
10	STAT3	chr4:100244965-100245142	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:100244984-100245153	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ADH1B	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10097	1.00[CEU][hapmap]
rs1631460	0.85[YRI][hapmap]
rs1662033	0.85[YRI][hapmap]
rs1662037	0.85[YRI][hapmap]
rs1662051	0.85[YRI][hapmap]
rs1662058	0.85[YRI][hapmap]
rs1662060	0.85[YRI][hapmap]
rs1693424	0.85[YRI][hapmap]
rs1693469	0.85[YRI][hapmap]
rs1693476	0.85[YRI][hapmap]
rs1693482	0.83[YRI][hapmap]
rs17028860	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1789903	0.85[YRI][hapmap]
rs1789911	0.85[YRI][hapmap]
rs1789920	0.85[YRI][hapmap]
rs1789921	0.85[YRI][hapmap]
rs1789924	0.85[YRI][hapmap]
rs2298755	0.85[YRI][hapmap]
rs3133158	0.85[YRI][hapmap]
rs34484723	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35365756	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs698	0.85[YRI][hapmap]
rs904095	0.85[YRI][hapmap]
rs904096	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3387812	chr4:100232775-100261923	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1002809	chr4:100234048-100285508	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3394945	chr4:100237238-100266245	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3465817	chr4:100238736-100267823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3465818	chr4:100238736-100267823	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr4:100239200-100245000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:100239200-100245200	Weak transcription	Left Ventricle	heart
3	chr4:100241600-100245000	Weak transcription	Aorta	Aorta
4	chr4:100242000-100245200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:100243200-100245000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:100243200-100245000	Weak transcription	Pancreas	Pancrea
7	chr4:100243200-100245200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:100243200-100245200	Weak transcription	Fetal Stomach	stomach
9	chr4:100243200-100245200	Weak transcription	Stomach Mucosa	stomach
10	chr4:100243200-100247400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:100243200-100250800	Weak transcription	Right Atrium	heart
12	chr4:100243400-100245400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:100243600-100245000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:100243600-100245200	Enhancers	Liver	Liver
15	chr4:100243600-100245800	Enhancers	Ovary	ovary
16	chr4:100244000-100246400	Enhancers	Psoas Muscle	Psoas
17	chr4:100244200-100247000	Enhancers	Adipose Nuclei	Adipose
18	chr4:100244400-100245600	Enhancers	Stomach Smooth Muscle	stomach
19	chr4:100244400-100246200	Enhancers	NHDF-Ad	bronchial
20	chr4:100244400-100247000	Enhancers	Fetal Lung	lung
21	chr4:100244400-100247200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:100244600-100245000	Weak transcription	NHLF	lung
23	chr4:100244600-100247000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:100244800-100245000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr4:100244800-100246800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links