Variant report

Variant	rs73402875
Chromosome Location	chr15:52427453-52427454
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	MAX	chr15:52427048-52428973	NB4	blood:	n/a	chr15:52427919-52427929

No.	Distal block	Cell Line	Cell type
1	chr15:52419606..52421639-chr15:52426759..52428564,2	K562	blood:
2	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
3	chr15:52420540..52423149-chr15:52426154..52427848,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259709	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10162634	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10162876	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10220890	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2231287	0.82[AFR][1000 genomes]
rs2414135	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28380149	0.83[ASN][1000 genomes]
rs28409853	0.94[ASN][1000 genomes]
rs28492876	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28499182	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28508167	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28631249	0.92[ASN][1000 genomes]
rs28678248	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28691169	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28703712	0.99[ASN][1000 genomes]
rs28716893	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28765241	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28835411	0.85[ASN][1000 genomes]
rs3751601	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3794539	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829469	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4238386	0.95[ASN][1000 genomes]
rs59851373	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61195644	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177966	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032818	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036771	0.98[EUR][1000 genomes];0.82[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
4	chr15:52406400-52427800	Weak transcription	Fetal Brain Male	brain
5	chr15:52407400-52427600	Weak transcription	HSMMtube	muscle
6	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
7	chr15:52407800-52428800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
9	chr15:52408800-52428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:52410000-52428600	Weak transcription	Hela-S3	cervix
11	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:52410600-52427800	Weak transcription	Adipose Nuclei	Adipose
13	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:52411200-52428600	Weak transcription	Left Ventricle	heart
15	chr15:52412000-52427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:52413600-52431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:52413800-52428400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:52414200-52427800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:52414400-52428400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:52416000-52427800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:52416000-52432800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:52416200-52431600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:52417000-52427600	Weak transcription	HSMM	muscle
26	chr15:52417000-52436000	Weak transcription	Lung	lung
27	chr15:52417200-52428600	Weak transcription	NHLF	lung
28	chr15:52417200-52428800	Weak transcription	Gastric	stomach
29	chr15:52417200-52431200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:52417200-52431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:52417200-52436200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr15:52417400-52429000	Weak transcription	K562	blood
33	chr15:52417400-52431800	Weak transcription	HMEC	breast
34	chr15:52417400-52432000	Weak transcription	NHDF-Ad	bronchial
35	chr15:52417600-52435400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:52417800-52431800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:52418200-52428000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:52418800-52427600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:52420200-52427800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:52420400-52433600	Strong transcription	Ovary	ovary
41	chr15:52421800-52431800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:52422000-52427600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:52422200-52427800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:52422200-52428200	Strong transcription	Primary T cells from cord blood	blood
45	chr15:52422200-52428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:52422400-52427600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:52422600-52431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:52423000-52458200	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links