Variant report

Variant	rs28409299
Chromosome Location	chr4:175418127-175418128
allele	A/G
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	chr4:175417693-175418257	A549	lung:	n/a	n/a
2	EP300	chr4:175417704-175418200	A549	lung:	n/a	n/a
3	FOXA2	chr4:175417661-175418234	A549	lung:	n/a	n/a
4	EP300	chr4:175417633-175418351	A549	lung:	n/a	chr4:175418319-175418328
5	FOSL2	chr4:175417701-175418216	A549	lung:	n/a	chr4:175417767-175417778
6	TCF12	chr4:175417661-175418416	A549	lung:	n/a	chr4:175417987-175417996
7	SP1	chr4:175417686-175418353	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175410591..175412440-chr4:175417791..175419375,2	K562	blood:

Variant related genes	Relation type
HPGD	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10027039	1.00[AMR][1000 genomes]
rs28510609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653442	1.00[AMR][1000 genomes]
rs9995652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525487	chr4:175400104-175470867	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv880289	chr4:175412975-175437117	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv881270	chr4:175413296-175425619	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175396000-175442800	Weak transcription	Esophagus	oesophagus
2	chr4:175409400-175424000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:175410000-175424600	Weak transcription	Fetal Stomach	stomach
4	chr4:175410000-175440800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:175410800-175420800	Weak transcription	Lung	lung
6	chr4:175410800-175425400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:175410800-175430800	Weak transcription	Gastric	stomach
8	chr4:175410800-175440000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:175411000-175418200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:175412000-175428400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:175412600-175418400	Strong transcription	Placenta	Placenta
12	chr4:175412800-175418200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:175413800-175418200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:175414400-175419000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:175414400-175428200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:175414600-175419000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:175415400-175424000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:175415600-175427600	Enhancers	Stomach Mucosa	stomach
19	chr4:175416400-175418400	Enhancers	Fetal Intestine Large	intestine
20	chr4:175416800-175418400	Enhancers	Fetal Intestine Small	intestine
21	chr4:175416800-175419200	Weak transcription	Fetal Thymus	thymus
22	chr4:175416800-175419600	Weak transcription	Small Intestine	intestine
23	chr4:175417000-175418400	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:175417200-175418800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:175417400-175418600	Enhancers	Primary hematopoietic stem cells	blood
26	chr4:175417600-175418600	Enhancers	Colon Smooth Muscle	Colon
27	chr4:175417600-175418600	Enhancers	Fetal Kidney	kidney
28	chr4:175417600-175418600	Flanking Active TSS	A549	lung
29	chr4:175417800-175418200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:175417800-175418400	Enhancers	Primary T cells from cord blood	blood
31	chr4:175417800-175418600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:175417800-175420000	Enhancers	Liver	Liver
33	chr4:175418000-175418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:175418000-175418400	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:175418000-175418600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr4:175418000-175418600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:175418000-175418600	Enhancers	Hela-S3	cervix
38	chr4:175418000-175438600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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