Variant report

Variant	rs2075533
Chromosome Location	chr9:117693631-117693632
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	chr9:117676811..117678604-chr9:117693310..117696147,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1006026	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10081728	0.96[EUR][1000 genomes]
rs10817682	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10817683	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10982445	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982456	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1126711	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12337739	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12338765	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12347977	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12352646	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1322054	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322056	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322059	0.85[EUR][1000 genomes]
rs1322060	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1322067	0.86[EUR][1000 genomes]
rs1407309	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2075534	0.84[EUR][1000 genomes]
rs2181033	0.82[EUR][1000 genomes]
rs2181036	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2295800	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2418324	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2418325	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2974	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3181197	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3181200	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3181201	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3181202	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3181348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3181367	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3181372	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3181374	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3789879	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4978611	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4979470	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4979471	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979472	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979473	0.97[EUR][1000 genomes]
rs6478117	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7025577	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7030090	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7032773	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs726656	0.85[EUR][1000 genomes]
rs726657	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7858603	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7872878	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs911603	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs927374	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs927375	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv6680	chr9:117690388-117699304	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2075533	ASTN2	cis	cerebellum	SCAN
rs2075533	KIAA1958	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117691800-117693800	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:117692400-117693800	Enhancers	Spleen	Spleen
3	chr9:117692600-117693800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr9:117692800-117695200	Enhancers	Fetal Lung	lung
5	chr9:117693000-117693800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:117693000-117694000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:117693200-117694200	Enhancers	Fetal Thymus	thymus
8	chr9:117693200-117697200	Weak transcription	Adipose Nuclei	Adipose
9	chr9:117693400-117693800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr9:117693400-117694000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:117693400-117694200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:117693400-117694200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:117693400-117694200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:117693400-117694400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr9:117693400-117694400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr9:117693400-117694400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:117693400-117694400	Flanking Active TSS	Thymus	Thymus
18	chr9:117693400-117695200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr9:117693600-117693800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:117693600-117693800	Enhancers	Primary B cells from cord blood	blood
21	chr9:117693600-117693800	Enhancers	Dnd41	blood
22	chr9:117693600-117693800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr9:117693600-117694000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr9:117693600-117694000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr9:117693600-117694200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
26	chr9:117693600-117694200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
27	chr9:117693600-117694200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
28	chr9:117693600-117694200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:117693600-117694200	Enhancers	Primary T cells from cord blood	blood
30	chr9:117693600-117694200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr9:117693600-117694400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
32	chr9:117693600-117694400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:117693600-117694400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr9:117693600-117694400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:117693600-117697200	Weak transcription	Right Atrium	heart

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