Variant report

Variant	rs9902509
Chromosome Location	chr17:38773947-38773948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38772991..38776371-chr17:38950027..38953549,4	MCF-7	breast:
2	chr17:38711199..38713464-chr17:38773822..38775935,2	MCF-7	breast:
3	chr17:38773571..38776015-chr17:38974880..38976971,2	MCF-7	breast:
4	chr17:38771673..38774769-chr17:38774806..38776457,3	K562	blood:
5	chr17:38773127..38778716-chr17:38801405..38806004,8	MCF-7	breast:
6	chr17:38722952..38724580-chr17:38773813..38776403,2	MCF-7	breast:
7	chr17:38773408..38778160-chr17:38801455..38807561,11	MCF-7	breast:
8	chr17:38716724..38718551-chr17:38772418..38774994,2	MCF-7	breast:
9	chr17:38763229..38767526-chr17:38771780..38775135,4	MCF-7	breast:
10	chr17:38732692..38734383-chr17:38772868..38775729,2	MCF-7	breast:
11	chr17:38588496..38590793-chr17:38771686..38774374,2	MCF-7	breast:
12	chr17:38765688..38767595-chr17:38773292..38775210,2	K562	blood:
13	chr17:38481166..38483354-chr17:38771299..38774149,2	MCF-7	breast:
14	chr17:38688685..38691278-chr17:38771780..38774213,2	MCF-7	breast:
15	chr17:38772124..38774636-chr17:38774789..38776541,3	MCF-7	breast:
16	chr17:38707503..38711120-chr17:38769935..38775644,8	MCF-7	breast:
17	chr17:38705642..38709928-chr17:38772338..38775854,5	MCF-7	breast:
18	chr17:38733163..38735894-chr17:38771819..38775610,4	MCF-7	breast:
19	chr17:38470862..38473621-chr17:38773618..38775413,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000126353	Chromatin interaction
ENSG00000073584	Chromatin interaction
ENSG00000167920	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11654834	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11659024	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474454	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16966093	0.87[ASN][1000 genomes]
rs55664118	0.93[ASN][1000 genomes]
rs6503545	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6503546	0.87[ASN][1000 genomes]
rs67138687	0.87[ASN][1000 genomes]
rs7218478	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7224919	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066541	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8074179	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9630727	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9630729	0.88[ASN][1000 genomes]
rs9894823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9902509	SMARCE1	cis	multi-tissue	Pritchard
rs9902509	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs9902509	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs9902509	KRT24	cis	Esophagus Mucosa	GTEx
rs9902509	ENSG00000073584	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38763400-38775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:38769600-38784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38770400-38774000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr17:38770600-38774000	Weak transcription	Right Atrium	heart
5	chr17:38770800-38776200	Enhancers	Placenta	Placenta
6	chr17:38771000-38775200	Weak transcription	Fetal Kidney	kidney
7	chr17:38771400-38774000	Weak transcription	Lung	lung
8	chr17:38771400-38775200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:38771600-38774200	Enhancers	Primary B cells from cord blood	blood
10	chr17:38771600-38774400	Enhancers	Primary B cells from peripheral blood	blood
11	chr17:38772000-38774000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr17:38772000-38776400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:38772000-38784600	Weak transcription	Gastric	stomach
14	chr17:38772000-38785000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:38772200-38774000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:38772200-38774200	Enhancers	Esophagus	oesophagus
17	chr17:38772200-38774200	Weak transcription	Fetal Intestine Large	intestine
18	chr17:38772200-38775000	Weak transcription	Liver	Liver
19	chr17:38772200-38775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:38772200-38776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:38772400-38774200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr17:38772400-38774400	Enhancers	GM12878-XiMat	blood
23	chr17:38772400-38775400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:38772400-38775400	Weak transcription	A549	lung
25	chr17:38772400-38776200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:38772400-38778800	Weak transcription	Spleen	Spleen
27	chr17:38772400-38783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr17:38772600-38774000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:38772600-38774000	Bivalent Enhancer	HepG2	liver
30	chr17:38772600-38774200	Weak transcription	Fetal Lung	lung
31	chr17:38772600-38774800	Enhancers	Fetal Stomach	stomach
32	chr17:38772600-38775400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr17:38772600-38775600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:38772600-38775800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:38772600-38785000	Weak transcription	Ovary	ovary
36	chr17:38772800-38774200	Enhancers	Colonic Mucosa	Colon
37	chr17:38772800-38775400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:38772800-38775400	Weak transcription	Fetal Thymus	thymus
39	chr17:38772800-38776000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:38773000-38784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:38773000-38786800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:38773200-38775800	Weak transcription	Primary T cells from cord blood	blood
43	chr17:38773400-38774400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr17:38773400-38775600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr17:38773600-38774000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr17:38773600-38774400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr17:38773600-38775400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:38773600-38775600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr17:38773600-38776000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr17:38773800-38774000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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