Variant report

Variant	rs7866392
Chromosome Location	chr9:92763235-92763236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:92761640..92763658-chr9:92766942..92769443,2	MCF-7	breast:
2	chr9:92216749..92221414-chr9:92756839..92763409,10	MCF-7	breast:
3	chr9:92756890..92759147-chr9:92762216..92764609,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GADD45G-5	chr9:92763074-92763500	XLOC_007451
2	lnc-GADD45G-5	chr9:92762923-92763500	XLOC_007451
3	lnc-GADD45G-5	chr9:92762923-92763500	NONHSAT132983
4	lnc-GADD45G-5	chr9:92762923-92763500	NONHSAT132986

No data

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10117261	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs10118552	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120740	0.84[ASN][1000 genomes]
rs10123198	0.80[ASN][1000 genomes]
rs10821386	0.80[CHB][hapmap]
rs10821474	0.82[YRI][hapmap]
rs10821475	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10821501	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993333	0.86[CHB][hapmap]
rs10993656	0.88[YRI][hapmap]
rs10993699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443364	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1999100	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6479580	0.81[ASN][1000 genomes]
rs652454	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs657899	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7021679	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025825	0.82[YRI][hapmap]
rs7038428	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs721833	0.81[ASN][1000 genomes]
rs7874166	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7866392	ROR2	cis	parietal	SCAN
rs7866392	SYK	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92753600-92765400	Enhancers	Fetal Intestine Large	intestine
2	chr9:92754000-92765400	Enhancers	Fetal Intestine Small	intestine
3	chr9:92757400-92770000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:92757600-92764200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:92757600-92770000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:92758800-92767600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:92760800-92766000	Enhancers	Fetal Brain Male	brain
8	chr9:92761200-92763600	Enhancers	Small Intestine	intestine
9	chr9:92761200-92765400	Enhancers	Fetal Thymus	thymus
10	chr9:92761200-92767400	Enhancers	Fetal Muscle Leg	muscle
11	chr9:92761600-92763600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:92761600-92763600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:92761600-92764600	Enhancers	Placenta	Placenta
14	chr9:92761600-92765200	Enhancers	Right Ventricle	heart
15	chr9:92761600-92765200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr9:92761600-92765600	Enhancers	Lung	lung
17	chr9:92761600-92765800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:92761600-92766400	Enhancers	Fetal Stomach	stomach
19	chr9:92761800-92763400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:92761800-92763600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:92761800-92763800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:92761800-92763800	Enhancers	Fetal Brain Female	brain
23	chr9:92761800-92766600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:92762200-92763400	Enhancers	Brain Angular Gyrus	brain
25	chr9:92762200-92764000	Weak transcription	Aorta	Aorta
26	chr9:92762400-92763600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:92762400-92763800	Enhancers	Brain Germinal Matrix	brain
28	chr9:92762400-92764000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:92762400-92764600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:92762400-92764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:92762400-92764600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr9:92762400-92765400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:92762400-92766600	Enhancers	Colon Smooth Muscle	Colon
34	chr9:92762600-92763400	Enhancers	Primary B cells from peripheral blood	blood
35	chr9:92762600-92763400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr9:92762600-92763400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr9:92762600-92763400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:92762600-92763400	Enhancers	Brain Cingulate Gyrus	brain
39	chr9:92762600-92763600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:92762600-92763600	Enhancers	Primary T cells from cord blood	blood
41	chr9:92762600-92763600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr9:92762600-92763600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr9:92762600-92763600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr9:92762600-92763600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr9:92762600-92763600	Enhancers	Adipose Nuclei	Adipose
46	chr9:92762600-92763600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr9:92762600-92763600	Enhancers	Fetal Kidney	kidney
48	chr9:92762600-92763600	Enhancers	NHDF-Ad	bronchial
49	chr9:92762600-92764200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:92762600-92764400	Enhancers	Primary monocytes fromperipheralblood	blood

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