Variant report

Variant	rs10121856
Chromosome Location	chr9:95736264-95736265
allele	C/T
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	EP300	chr9:95736252-95737152	MCF-7	breast:	n/a	n/a
2	NR2F2	chr9:95736153-95737389	MCF-7	breast:	n/a	n/a
3	GATA3	chr9:95736143-95737570	MCF-7	breast:	n/a	n/a
4	TCF7L2	chr9:95736228-95736730	MCF-7	breast:	n/a	chr9:95736491-95736505 chr9:95736494-95736501
5	NR2F2	chr9:95736191-95736915	MCF-7	breast:	n/a	n/a
6	GATA3	chr9:95736248-95737180	MCF-7	breast:	n/a	n/a
7	HDAC2	chr9:95736200-95737211	MCF-7	breast:	n/a	n/a
8	MAX	chr9:95735816-95737628	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95733025..95737240-chr9:95894074..95898257,5	MCF-7	breast:

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

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10283714	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739940	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821046	0.90[GIH][hapmap];0.81[MEX][hapmap]
rs10821048	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]
rs10821049	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821050	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821051	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992561	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10992564	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11788120	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802381	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3936099	0.90[GIH][hapmap];0.81[MEX][hapmap]
rs4302906	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744159	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744161	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7026624	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs7030160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7032953	0.82[EUR][1000 genomes]
rs7847879	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7848528	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7850247	0.82[CEU][hapmap]
rs7867742	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7869056	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7869421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7870077	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7875497	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9942903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9942965	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10121856	FGD3	cis	Skin Sun Exposed Lower leg	GTEx
rs10121856	ZNF484	cis	parietal	SCAN
rs10121856	ZNF484	cis	cerebellum	SCAN
rs10121856	SUSD3	cis	multi-tissue	Pritchard

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95728200-95739600	Weak transcription	Fetal Stomach	stomach
2	chr9:95728800-95739400	Weak transcription	Gastric	stomach
3	chr9:95728800-95739600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:95728800-95740600	Weak transcription	Small Intestine	intestine
5	chr9:95729000-95739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:95729000-95741400	Weak transcription	Right Ventricle	heart
7	chr9:95729200-95739200	Weak transcription	Colonic Mucosa	Colon
8	chr9:95731600-95736800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:95732000-95741200	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:95732800-95737400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:95733200-95736600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:95733200-95736600	Weak transcription	HMEC	breast
13	chr9:95733200-95736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:95733200-95736800	Weak transcription	Spleen	Spleen
15	chr9:95733400-95737200	Weak transcription	Brain Germinal Matrix	brain
16	chr9:95733400-95741400	Weak transcription	Fetal Brain Female	brain
17	chr9:95733400-95742000	Weak transcription	Fetal Brain Male	brain
18	chr9:95733600-95736800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:95733600-95736800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr9:95733600-95736800	Weak transcription	Fetal Lung	lung
21	chr9:95733600-95738000	Weak transcription	Esophagus	oesophagus
22	chr9:95733800-95736800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:95733800-95736800	Weak transcription	Dnd41	blood
24	chr9:95733800-95737200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:95733800-95739400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:95734000-95736800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:95734200-95736800	Weak transcription	Lung	lung
28	chr9:95734200-95737800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:95735000-95736600	Enhancers	Fetal Intestine Large	intestine
30	chr9:95735000-95739800	Enhancers	Placenta	Placenta
31	chr9:95735400-95736400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:95735400-95736600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr9:95735400-95752600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr9:95735600-95737400	Weak transcription	GM12878-XiMat	blood
35	chr9:95735600-95740200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr9:95735800-95736400	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr9:95735800-95736400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr9:95735800-95736800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr9:95735800-95736800	Enhancers	Pancreas	Pancrea
40	chr9:95735800-95737000	Enhancers	Duodenum Mucosa	Duodenum
41	chr9:95735800-95737200	Enhancers	HepG2	liver
42	chr9:95735800-95737400	Enhancers	Fetal Intestine Small	intestine
43	chr9:95735800-95739600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:95735800-95739600	Strong transcription	Fetal Thymus	thymus
45	chr9:95735800-95740000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:95735800-95740200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:95735800-95740200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:95735800-95740400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:95735800-95742200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr9:95736000-95736600	Genic enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links