Variant report

Variant	rs17239770
Chromosome Location	chr15:57790436-57790437
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57627655..57630463-chr15:57790410..57793260,2	K562	blood:
2	chr15:57785599..57788871-chr15:57789912..57793304,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11629589	0.96[ASN][1000 genomes]
rs11857299	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441608	0.88[ASN][1000 genomes]
rs1280381	0.91[EUR][1000 genomes]
rs17239763	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2922224	0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4774266	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774947	0.94[ASN][1000 genomes]
rs4774948	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7168095	0.82[YRI][hapmap]
rs7170267	0.88[LWK][hapmap];0.86[YRI][hapmap]
rs932029	0.81[CHB][hapmap]
rs966693	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv457170	chr15:57644456-57790436	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv569588	chr15:57644456-57790436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1045620	chr15:57680733-57804237	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2763103	chr15:57781577-57799765	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17239770	WDR72	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57771000-57795200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57778200-57798400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:57779000-57794200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:57779000-57794400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:57779000-57797600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:57779000-57798200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:57779400-57794200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:57779400-57800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:57787000-57791000	Enhancers	Pancreas	Pancrea
10	chr15:57787200-57790600	Enhancers	Stomach Mucosa	stomach
11	chr15:57787200-57802000	Weak transcription	Aorta	Aorta
12	chr15:57787400-57790600	Enhancers	Fetal Intestine Small	intestine
13	chr15:57787400-57791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:57787600-57793000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:57787800-57791400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:57787800-57793200	Weak transcription	NHDF-Ad	bronchial
17	chr15:57788200-57790600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:57788200-57793400	Weak transcription	HUVEC	blood vessel
19	chr15:57788200-57797600	Enhancers	Fetal Heart	heart
20	chr15:57788400-57791400	Enhancers	Lung	lung
21	chr15:57788400-57793600	Weak transcription	Ovary	ovary
22	chr15:57788600-57792800	Weak transcription	Fetal Kidney	kidney
23	chr15:57789200-57793000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:57789400-57796200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:57789800-57801600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:57790000-57792000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:57790000-57792200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:57790000-57792200	Weak transcription	Right Atrium	heart
29	chr15:57790000-57792400	Weak transcription	Right Ventricle	heart
30	chr15:57790000-57793400	Weak transcription	Liver	Liver
31	chr15:57790000-57794400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:57790000-57794800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:57790000-57796800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:57790000-57797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:57790000-57808600	Weak transcription	Fetal Brain Male	brain
36	chr15:57790200-57791200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:57790200-57793400	Weak transcription	Esophagus	oesophagus
38	chr15:57790200-57793400	Weak transcription	Placenta	Placenta
39	chr15:57790200-57793600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:57790200-57793800	Weak transcription	Fetal Intestine Large	intestine
41	chr15:57790200-57794200	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:57790200-57794400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:57790200-57794400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:57790200-57797600	Weak transcription	Brain Anterior Caudate	brain
45	chr15:57790200-57799000	Enhancers	HepG2	liver
46	chr15:57790200-57801400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:57790400-57790800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:57790400-57790800	Weak transcription	Gastric	stomach
49	chr15:57790400-57792200	Weak transcription	Fetal Stomach	stomach
50	chr15:57790400-57793200	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links