Variant report

Variant	rs10992580
Chromosome Location	chr9:95780909-95780910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95780776..95784501-chr9:95797559..95801380,3	MCF-7	breast:
2	chr9:95773730..95778717-chr9:95778943..95783002,4	K562	blood:
3	chr9:95770628..95772439-chr9:95778625..95781372,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10992556	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs10992557	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10992569	0.93[EUR][1000 genomes]
rs10992576	0.89[EUR][1000 genomes]
rs10992577	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992578	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992579	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992584	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992586	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992587	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992588	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992599	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992601	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992605	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10992607	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12377562	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12380201	0.93[EUR][1000 genomes]
rs12380291	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12380789	0.93[EUR][1000 genomes]
rs41273404	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55654224	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs72741052	0.93[EUR][1000 genomes]
rs72741055	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741057	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741060	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72741063	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9696630	0.85[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992580	FGD3	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95761600-95785800	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:95761600-95785800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:95762000-95786400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:95762600-95790200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:95763600-95787200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:95763800-95789400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:95766400-95785600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr9:95766600-95783400	Weak transcription	Placenta	Placenta
9	chr9:95766600-95790400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:95766600-95790800	Weak transcription	Right Ventricle	heart
11	chr9:95766600-95791000	Weak transcription	Colonic Mucosa	Colon
12	chr9:95766600-95791000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:95766600-95794000	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:95766800-95782400	Weak transcription	Liver	Liver
15	chr9:95766800-95786400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:95767000-95781800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:95767000-95787200	Strong transcription	Fetal Thymus	thymus
18	chr9:95767200-95781600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:95767400-95781800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:95767400-95782000	Strong transcription	Primary T cells from cord blood	blood
21	chr9:95769000-95781600	Weak transcription	Adipose Nuclei	Adipose
22	chr9:95770200-95793600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:95772600-95781200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:95772600-95783000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:95773400-95781600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:95773400-95781800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr9:95773400-95786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:95773600-95783000	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:95774200-95783800	Weak transcription	Fetal Brain Male	brain
30	chr9:95774800-95788400	Strong transcription	Thymus	Thymus
31	chr9:95775000-95786600	Strong transcription	Primary B cells from cord blood	blood
32	chr9:95776400-95783200	Weak transcription	Fetal Brain Female	brain
33	chr9:95776600-95781600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:95776600-95781600	Weak transcription	Fetal Intestine Small	intestine
35	chr9:95776600-95781600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:95776600-95799200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:95776600-95799400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:95776800-95783200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:95778000-95781600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:95778000-95782200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:95778000-95786600	Strong transcription	Spleen	Spleen
42	chr9:95778200-95781600	Weak transcription	GM12878-XiMat	blood
43	chr9:95778400-95783200	Weak transcription	Esophagus	oesophagus
44	chr9:95778600-95782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:95778600-95783000	Weak transcription	Fetal Stomach	stomach
46	chr9:95778600-95786400	Weak transcription	Gastric	stomach
47	chr9:95779000-95783600	Weak transcription	Small Intestine	intestine
48	chr9:95779600-95785800	Strong transcription	Fetal Intestine Large	intestine
49	chr9:95779600-95786600	Strong transcription	Dnd41	blood
50	chr9:95779600-95788800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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