Variant report

Variant	rs2787398
Chromosome Location	chr9:102931623-102931624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102926106..102928725-chr9:102930778..102932708,2	MCF-7	breast:
2	chr9:102917410..102919352-chr9:102930134..102931648,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16918878	0.80[ASN][1000 genomes]
rs16918892	0.80[ASN][1000 genomes]
rs2209081	0.95[ASN][1000 genomes]
rs7020636	0.91[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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2787398	STX17	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102874200-102937600	Weak transcription	Aorta	Aorta
2	chr9:102879800-102935000	Weak transcription	Ovary	ovary
3	chr9:102883000-102937600	Weak transcription	Fetal Intestine Large	intestine
4	chr9:102885200-102932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:102889200-102936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:102889600-102934600	Weak transcription	Fetal Intestine Small	intestine
7	chr9:102891800-102935200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:102893000-102934600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:102893800-102936200	Weak transcription	Primary B cells from cord blood	blood
10	chr9:102912400-102937800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:102912800-102936200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:102913200-102935400	Weak transcription	Fetal Lung	lung
13	chr9:102914400-102932000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:102914600-102940600	Weak transcription	HSMMtube	muscle
15	chr9:102915200-102934800	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:102915200-102935400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:102916200-102935400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:102916200-102941400	Weak transcription	HepG2	liver
19	chr9:102916400-102932400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:102916400-102934800	Weak transcription	Left Ventricle	heart
21	chr9:102916400-102938200	Weak transcription	Adipose Nuclei	Adipose
22	chr9:102917400-102935000	Weak transcription	Liver	Liver
23	chr9:102917400-102936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:102919400-102936000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:102920600-102936000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:102921200-102934800	Weak transcription	Psoas Muscle	Psoas
27	chr9:102921200-102938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:102922600-102935200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:102922800-102935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:102922800-102936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:102924200-102935400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:102928600-102934800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr9:102929000-102935000	Weak transcription	Primary T cells from cord blood	blood
34	chr9:102929600-102938000	Weak transcription	Thymus	Thymus
35	chr9:102929800-102932200	Weak transcription	HUVEC	blood vessel
36	chr9:102930400-102932600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:102930400-102937600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:102930600-102940000	Weak transcription	Pancreas	Pancrea
39	chr9:102930800-102932000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:102930800-102938000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:102931000-102934000	Weak transcription	A549	lung
42	chr9:102931000-102934800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:102931000-102936400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:102931000-102941000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:102931200-102936000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:102931400-102935200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links