Variant report

Variant	rs10992569
Chromosome Location	chr9:95753946-95753947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95750295..95753959-chr9:95856034..95859427,4	MCF-7	breast:
2	chr9:95746898..95754225-chr9:95890814..95897960,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10992576	0.83[EUR][1000 genomes]
rs10992577	0.93[EUR][1000 genomes]
rs10992578	0.93[EUR][1000 genomes]
rs10992579	0.93[EUR][1000 genomes]
rs10992580	0.93[EUR][1000 genomes]
rs10992584	0.90[EUR][1000 genomes]
rs10992586	0.90[EUR][1000 genomes]
rs10992587	0.90[EUR][1000 genomes]
rs10992588	0.90[EUR][1000 genomes]
rs10992599	0.90[EUR][1000 genomes]
rs12377562	1.00[EUR][1000 genomes]
rs12380201	1.00[EUR][1000 genomes]
rs12380291	0.90[EUR][1000 genomes]
rs12380789	1.00[EUR][1000 genomes]
rs41273404	0.87[EUR][1000 genomes]
rs55654224	0.90[EUR][1000 genomes]
rs7043408	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741049	0.87[EUR][1000 genomes]
rs72741052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741055	0.93[EUR][1000 genomes]
rs72741057	0.93[EUR][1000 genomes]
rs72741060	0.90[EUR][1000 genomes]
rs72741063	0.90[EUR][1000 genomes]
rs9696630	0.90[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992569	FGD3	cis	Whole Blood	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95740000-95754800	Weak transcription	Gastric	stomach
2	chr9:95740000-95754800	Weak transcription	Pancreas	Pancrea
3	chr9:95747800-95754600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:95748200-95756000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:95749200-95755600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:95750200-95754800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:95750600-95754400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr9:95750600-95754800	Weak transcription	Spleen	Spleen
9	chr9:95750600-95755000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:95750800-95754600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:95750800-95754600	Weak transcription	GM12878-XiMat	blood
12	chr9:95750800-95754800	Weak transcription	Lung	lung
13	chr9:95751200-95754600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:95751200-95755000	Weak transcription	Esophagus	oesophagus
15	chr9:95751400-95754200	Weak transcription	Dnd41	blood
16	chr9:95751400-95754400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr9:95751600-95754600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr9:95751800-95754800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:95751800-95755600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:95752000-95754200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:95752200-95754200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:95752400-95754600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:95752400-95755400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:95752400-95755600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr9:95752600-95754400	Enhancers	Primary T cells from cord blood	blood
26	chr9:95752600-95754600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr9:95752600-95754800	Weak transcription	Fetal Thymus	thymus
28	chr9:95752600-95755600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr9:95752600-95766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:95752800-95754800	Weak transcription	Thymus	Thymus
31	chr9:95753000-95754200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:95753200-95754000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr9:95753200-95754200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:95753200-95754400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:95753200-95754400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr9:95753200-95755600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:95753400-95754600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:95753400-95754800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr9:95753400-95755800	Strong transcription	Primary B cells from cord blood	blood
40	chr9:95753600-95754800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:95753600-95754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:95753800-95754200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:95753800-95754600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr9:95753800-95754800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr9:95753800-95756000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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