Variant report

Variant	rs17335265
Chromosome Location	chr9:100390627-100390628
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	chr9:100377919..100379594-chr9:100390276..100392003,2	MCF-7	breast:
2	chr9:100390249..100392678-chr9:100424197..100427022,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10116536	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10119687	0.96[CEU][hapmap];1.00[TSI][hapmap]
rs10120102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10123969	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983405	1.00[ASN][1000 genomes]
rs12344605	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346336	1.00[ASN][1000 genomes]
rs12349178	1.00[ASN][1000 genomes]
rs16923269	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs16923677	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs16923719	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176639	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284139	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480232	0.96[CEU][hapmap]
rs4617277	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751548	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849509	1.00[ASN][1000 genomes]
rs952765	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17335265	ZNF169	cis	cerebellum	SCAN
rs17335265	FBP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:100363000-100394600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:100368200-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:100368200-100394200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:100368400-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:100372800-100394000	Weak transcription	Colonic Mucosa	Colon
7	chr9:100374000-100394000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:100374600-100393800	Weak transcription	Fetal Kidney	kidney
9	chr9:100377400-100394000	Weak transcription	NHEK	skin
10	chr9:100380400-100394400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:100381800-100394200	Weak transcription	HSMMtube	muscle
12	chr9:100384000-100391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:100384200-100391000	Weak transcription	Right Atrium	heart
14	chr9:100384200-100394000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:100384200-100394000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:100385000-100391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:100385000-100391000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:100385000-100391000	Weak transcription	Spleen	Spleen
19	chr9:100385000-100393800	Weak transcription	Fetal Intestine Small	intestine
20	chr9:100385000-100394600	Weak transcription	Lung	lung
21	chr9:100385200-100393800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:100385400-100391200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:100385600-100391000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:100386000-100394200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:100386400-100391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:100386600-100391000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:100386800-100391000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:100386800-100391400	Weak transcription	Gastric	stomach
29	chr9:100386800-100393600	Weak transcription	Fetal Stomach	stomach
30	chr9:100387000-100393400	Weak transcription	Fetal Brain Male	brain
31	chr9:100387800-100393800	Weak transcription	HMEC	breast
32	chr9:100388000-100392400	Enhancers	Fetal Heart	heart
33	chr9:100388000-100393600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr9:100388000-100394200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:100388000-100394200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:100388200-100390800	Weak transcription	Fetal Brain Female	brain
37	chr9:100388200-100391000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr9:100388200-100391000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:100388200-100391000	Weak transcription	Brain Substantia Nigra	brain
40	chr9:100388200-100391000	Weak transcription	Pancreas	Pancrea
41	chr9:100388200-100391200	Weak transcription	Brain Anterior Caudate	brain
42	chr9:100388200-100391400	Weak transcription	Brain Angular Gyrus	brain
43	chr9:100388200-100393200	Weak transcription	K562	blood
44	chr9:100388200-100393600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:100388200-100393800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:100388200-100393800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:100388200-100393800	Weak transcription	Adipose Nuclei	Adipose
48	chr9:100388200-100393800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:100388200-100394000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:100388200-100394000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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