Variant report

Variant	rs10821048
Chromosome Location	chr9:95732546-95732547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr9:95732522-95732976	T-47D	breast:	n/a	n/a
2	E2F6	chr9:95732446-95733339	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr9:95732449-95733204	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr9:95732467-95733178	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr9:95732424-95733214	ECC-1	luminal epithelium:	n/a	n/a
6	FOXA1	chr9:95732453-95732970	T-47D	breast:	n/a	n/a
7	ESR1	chr9:95732432-95732821	T-47D	breast:	n/a	n/a
8	TEAD4	chr9:95732457-95733216	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA3	chr9:95732412-95732812	T-47D	breast:	n/a	n/a
10	ESR1	chr9:95732244-95732732	T-47D	breast:	n/a	n/a
11	USF1	chr9:95732525-95733211	ECC-1	luminal epithelium:	n/a	n/a
12	ESR1	chr9:95732279-95732803	T-47D	breast:	n/a	n/a
13	MAX	chr9:95732399-95733170	ECC-1	luminal epithelium:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
14	MAX	chr9:95732473-95733264	MCF-7	breast:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
15	EP300	chr9:95732407-95732884	T-47D	breast:	n/a	n/a
16	POLR2A	chr9:95732472-95732973	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr9:95732469-95732815	U87	brain:	n/a	n/a
18	CHD2	chr9:95732517-95733089	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUND	chr9:95732384-95733367	H1-hESC	embryonic stem cell:	n/a	chr9:95733315-95733324
20	ESR1	chr9:95732281-95732834	T-47D	breast:	n/a	n/a
21	MAX	chr9:95732432-95733218	H1-hESC	embryonic stem cell:	n/a	chr9:95733048-95733058 chr9:95733062-95733072
22	SP1	chr9:95732486-95733130	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95731583..95735118-chr9:95737800..95740218,3	K562	blood:
2	chr9:95731272..95732964-chr9:95895470..95897455,2	MCF-7	breast:
3	chr9:95725342..95729207-chr9:95729946..95733070,3	K562	blood:
4	chr9:95617721..95619432-chr9:95731199..95733428,2	MCF-7	breast:
5	chr9:95637654..95640681-chr9:95731798..95734856,3	MCF-7	breast:

Variant related genes	Relation type
FGD3	TF binding region
ENSG00000127081	Chromatin interaction
ENSG00000127084	Chromatin interaction
ENSG00000131669	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10121856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10283714	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821049	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821050	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821051	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992561	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11788120	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3802381	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4302906	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744159	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744161	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7030160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7032953	0.82[EUR][1000 genomes]
rs7847879	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7848528	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7850247	0.82[CEU][hapmap]
rs7867742	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7869056	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7869421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7870077	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7875497	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9942903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9942965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][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
rs10821048	FGD3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95725600-95734000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr9:95728000-95733800	Weak transcription	Right Atrium	heart
3	chr9:95728200-95739600	Weak transcription	Fetal Stomach	stomach
4	chr9:95728600-95732600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:95728600-95733200	Genic enhancers	Spleen	Spleen
6	chr9:95728800-95732800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:95728800-95732800	Weak transcription	Brain Substantia Nigra	brain
8	chr9:95728800-95733600	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:95728800-95733800	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr9:95728800-95739400	Weak transcription	Gastric	stomach
11	chr9:95728800-95739600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:95728800-95740600	Weak transcription	Small Intestine	intestine
13	chr9:95729000-95733800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:95729000-95734000	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:95729000-95735000	Weak transcription	Adipose Nuclei	Adipose
16	chr9:95729000-95739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:95729000-95741400	Weak transcription	Right Ventricle	heart
18	chr9:95729200-95733800	Genic enhancers	Thymus	Thymus
19	chr9:95729200-95734000	Genic enhancers	Fetal Thymus	thymus
20	chr9:95729200-95739200	Weak transcription	Colonic Mucosa	Colon
21	chr9:95729400-95733800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr9:95729600-95734200	Genic enhancers	Primary B cells from cord blood	blood
23	chr9:95730000-95733600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr9:95730200-95733000	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:95730400-95733800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
26	chr9:95730600-95732800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
27	chr9:95730600-95733400	Enhancers	Brain Germinal Matrix	brain
28	chr9:95730600-95733800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:95731000-95733200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:95731000-95733200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:95731000-95734000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:95731000-95734200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:95731200-95733000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr9:95731200-95733000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:95731200-95733600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr9:95731200-95733600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:95731200-95733800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95731200-95733800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:95731200-95733800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:95731200-95734000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr9:95731200-95735000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr9:95731400-95732600	Weak transcription	GM12878-XiMat	blood
43	chr9:95731400-95733000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
44	chr9:95731400-95733200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr9:95731400-95733400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:95731400-95733600	Enhancers	Duodenum Mucosa	Duodenum
47	chr9:95731400-95733800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr9:95731400-95733800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:95731400-95734000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:95731400-95734200	Enhancers	HUES64 Cell Line	embryonic stem cell

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