Variant report

Variant	rs10992556
Chromosome Location	chr9:95728914-95728915
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	chr9:95726879..95729699-chr9:95735044..95738591,3	K562	blood:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10992543	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992544	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992557	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992580	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs10992587	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs10992599	0.85[CEU][hapmap]
rs12377272	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12377562	0.82[YRI][hapmap]
rs12378192	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12378898	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12380201	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12380291	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7043408	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs72741032	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741034	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72741039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741043	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72741045	1.00[EUR][1000 genomes]
rs72741049	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992556	FGD3	cis	multi-tissue	Pritchard

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95715400-95732200	Weak transcription	Fetal Brain Female	brain
2	chr9:95720000-95731400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:95725600-95729200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr9:95725600-95734000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr9:95725800-95729000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:95725800-95729200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr9:95726400-95729000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:95726400-95729000	Active TSS	Esophagus	oesophagus
9	chr9:95726400-95730200	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr9:95726600-95729000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:95726600-95729000	Active TSS	Liver	Liver
12	chr9:95726600-95729000	Active TSS	Placenta	Placenta
13	chr9:95726600-95730600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:95726600-95731400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:95726800-95731200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:95726800-95731200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:95726800-95732200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:95727000-95729800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
19	chr9:95727000-95729800	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr9:95727200-95729200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr9:95727400-95729000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:95727400-95729000	Enhancers	Right Ventricle	heart
23	chr9:95727400-95729600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:95727800-95729000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr9:95728000-95729000	Transcr. at gene 5' and 3'	Thymus	Thymus
26	chr9:95728000-95729400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr9:95728000-95732400	Weak transcription	Left Ventricle	heart
28	chr9:95728000-95733800	Weak transcription	Right Atrium	heart
29	chr9:95728200-95729000	Enhancers	Fetal Intestine Large	intestine
30	chr9:95728200-95729000	Enhancers	Lung	lung
31	chr9:95728200-95729200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr9:95728200-95729200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
33	chr9:95728200-95731200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:95728200-95739600	Weak transcription	Fetal Stomach	stomach
35	chr9:95728400-95729000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:95728400-95729000	Enhancers	Adipose Nuclei	Adipose
37	chr9:95728400-95729200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:95728400-95729200	Active TSS	Colonic Mucosa	Colon
39	chr9:95728400-95730600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:95728400-95731200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:95728400-95731200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:95728400-95732400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:95728600-95729000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr9:95728600-95729000	Enhancers	Pancreas	Pancrea
45	chr9:95728600-95729200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
46	chr9:95728600-95729200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:95728600-95729600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
48	chr9:95728600-95729800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr9:95728600-95730600	Weak transcription	Brain Germinal Matrix	brain
50	chr9:95728600-95731000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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