Variant report

Variant	rs10116422
Chromosome Location	chr9:96357739-96357740
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96355442..96358084-chr9:96410672..96413121,3	MCF-7	breast:
2	chr9:96356589..96359432-chr9:96360730..96362532,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10114002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117225	0.82[CHD][hapmap]
rs10117691	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10123378	0.82[CHD][hapmap]
rs10156602	0.81[TSI][hapmap]
rs10761238	0.85[CEU][hapmap];0.80[CHD][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10761240	0.82[CHD][hapmap]
rs10821160	0.81[CEU][hapmap]
rs10821163	0.82[CEU][hapmap]
rs10821168	0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs10821181	0.81[CEU][hapmap]
rs10992792	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992797	0.82[CHD][hapmap]
rs13294381	0.85[EUR][1000 genomes]
rs1412048	0.81[CHD][hapmap]
rs4568663	0.82[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10116422	FAM120AOS	cis	parietal	SCAN
rs10116422	SUSD3	cis	parietal	SCAN
rs10116422	HIATL1	cis	parietal	SCAN
rs10116422	DIRAS2	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96341600-96359600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:96341800-96362200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:96342200-96359600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:96342600-96357800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:96343400-96360600	Weak transcription	Dnd41	blood
6	chr9:96345000-96362600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:96347400-96359000	Enhancers	Left Ventricle	heart
8	chr9:96347600-96360600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:96348400-96360200	Weak transcription	Primary B cells from cord blood	blood
10	chr9:96348400-96360200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:96351400-96359600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:96352400-96358400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:96352400-96358600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:96352400-96360200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:96352400-96361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:96352400-96384600	Weak transcription	NHLF	lung
20	chr9:96352600-96358800	Weak transcription	Primary T cells from cord blood	blood
21	chr9:96352600-96362400	Weak transcription	Fetal Lung	lung
22	chr9:96352800-96358200	Weak transcription	Aorta	Aorta
23	chr9:96352800-96360600	Weak transcription	Thymus	Thymus
24	chr9:96352800-96360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:96353000-96360000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:96353000-96360400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:96353400-96360000	Weak transcription	Brain Germinal Matrix	brain
28	chr9:96354200-96361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:96354400-96360000	Weak transcription	Fetal Brain Female	brain
30	chr9:96354600-96359800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:96355000-96361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:96355200-96357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:96355200-96359600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:96355200-96359800	Weak transcription	Brain Anterior Caudate	brain
35	chr9:96355200-96360000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:96355200-96360400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:96355200-96360400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:96355200-96362600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:96355200-96362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:96355200-96362800	Weak transcription	Brain Angular Gyrus	brain
41	chr9:96355400-96360600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:96355400-96361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:96355400-96361400	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:96355600-96358200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr9:96355600-96360000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:96355600-96360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:96355600-96360600	Weak transcription	HepG2	liver
48	chr9:96356200-96357800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:96356200-96358400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:96356200-96360200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links