Variant report

Variant	rs17719089
Chromosome Location	chr10:116383343-116383344
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	chr10:116381677..116383578-chr10:116393467..116395747,2	MCF-7	breast:
2	chr10:116310031..116311847-chr10:116382346..116385171,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10885589	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1109267	0.87[ASW][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11196807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196819	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11196828	0.87[ASW][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11599283	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12220330	0.85[AMR][1000 genomes]
rs12570718	0.82[GIH][hapmap];0.83[LWK][hapmap]
rs12776647	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4568917	0.82[GIH][hapmap];0.89[LWK][hapmap]
rs4752043	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904491	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17719089	PDCD4	cis	parietal	SCAN
rs17719089	HABP2	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116372000-116383600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:116378200-116385000	Enhancers	Right Atrium	heart
3	chr10:116378800-116391200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:116379600-116383600	Weak transcription	Aorta	Aorta
5	chr10:116379600-116383600	Enhancers	Fetal Heart	heart
6	chr10:116380000-116384200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:116381200-116385000	Enhancers	Left Ventricle	heart
8	chr10:116381400-116383400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:116381400-116385200	Enhancers	Stomach Mucosa	stomach
10	chr10:116381800-116383400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:116381800-116383400	Enhancers	Ovary	ovary
12	chr10:116382000-116383400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr10:116382000-116384000	Weak transcription	Pancreas	Pancrea
14	chr10:116382000-116384400	Enhancers	Gastric	stomach
15	chr10:116382000-116385000	Weak transcription	Right Ventricle	heart
16	chr10:116382000-116385600	Enhancers	HepG2	liver
17	chr10:116382200-116383600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr10:116382200-116383600	Enhancers	Fetal Kidney	kidney
19	chr10:116382200-116384000	Enhancers	Adipose Nuclei	Adipose
20	chr10:116382200-116384200	Weak transcription	Esophagus	oesophagus
21	chr10:116382200-116384400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:116382200-116384400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr10:116382200-116384400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr10:116382200-116385000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr10:116382400-116383400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:116382400-116383400	Enhancers	Brain Anterior Caudate	brain
27	chr10:116382400-116383800	Enhancers	Duodenum Mucosa	Duodenum
28	chr10:116382400-116384000	Enhancers	Fetal Intestine Small	intestine
29	chr10:116382400-116384200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:116382400-116384200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr10:116382400-116384200	Enhancers	Colon Smooth Muscle	Colon
32	chr10:116382400-116384400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr10:116382400-116384400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr10:116382400-116384400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr10:116382400-116384400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:116382400-116384400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:116382400-116384400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr10:116382400-116384400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:116382400-116384400	Enhancers	Stomach Smooth Muscle	stomach
40	chr10:116382400-116384600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr10:116382400-116385400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr10:116382400-116385600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr10:116382400-116387400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:116382400-116387600	Enhancers	HMEC	breast
45	chr10:116382400-116387800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:116382400-116388000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr10:116382600-116383400	Enhancers	Fetal Intestine Large	intestine
48	chr10:116382600-116383800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:116382600-116384200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr10:116382600-116384400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links