Variant report

Variant	rs17027485
Chromosome Location	chr4:152180644-152180645
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	chr4:152180615-152180751	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:152180009-152180910	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000249012	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17027482	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027505	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17027509	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17027521	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs17027540	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2407219	0.97[AFR][1000 genomes]
rs41520344	0.80[AFR][1000 genomes]
rs60499080	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
4	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:152149200-152185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:152158800-152181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:152172200-152183400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:152172200-152184000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:152172200-152184000	Weak transcription	Lung	lung
9	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:152173000-152184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:152173400-152189400	Weak transcription	Aorta	Aorta
12	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:152174000-152187200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:152174200-152183200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:152174200-152183400	Weak transcription	Right Atrium	heart
17	chr4:152174200-152183600	Weak transcription	Brain Anterior Caudate	brain
18	chr4:152174400-152183800	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:152174600-152181800	Weak transcription	Left Ventricle	heart
20	chr4:152174600-152182400	Weak transcription	Psoas Muscle	Psoas
21	chr4:152175200-152183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:152177400-152187600	Weak transcription	Fetal Intestine Large	intestine
23	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:152177800-152183400	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:152177800-152183600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:152178200-152188200	Weak transcription	Liver	Liver
28	chr4:152178800-152180800	Strong transcription	Fetal Intestine Small	intestine
29	chr4:152178800-152181600	Enhancers	Fetal Heart	heart
30	chr4:152179000-152181600	Weak transcription	NHEK	skin
31	chr4:152179400-152180800	Enhancers	Right Ventricle	heart
32	chr4:152179400-152183600	Weak transcription	Brain Substantia Nigra	brain
33	chr4:152179600-152181000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:152179600-152182800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:152180000-152183600	Weak transcription	Ovary	ovary
36	chr4:152180000-152193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:152180200-152181000	Strong transcription	HepG2	liver
38	chr4:152180200-152189000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:152180600-152180800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr4:152180600-152180800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:152180600-152180800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:152180600-152180800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:152180600-152181600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:152180600-152183600	Weak transcription	Fetal Stomach	stomach

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