Variant report

Variant	rs3789879
Chromosome Location	chr9:117678236-117678237
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	chr9:117676811..117678604-chr9:117693310..117696147,2	MCF-7	breast:
2	chr9:117677998..117681403-chr9:117681907..117683952,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1006025	0.83[EUR][1000 genomes]
rs1006026	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1006027	0.83[EUR][1000 genomes]
rs10081728	0.84[EUR][1000 genomes]
rs10817679	0.88[ASN][1000 genomes]
rs10817682	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817683	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10817685	0.81[EUR][1000 genomes]
rs10982445	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982449	0.83[EUR][1000 genomes]
rs10982450	0.85[EUR][1000 genomes]
rs10982451	0.84[EUR][1000 genomes]
rs10982453	0.83[EUR][1000 genomes]
rs10982454	0.83[EUR][1000 genomes]
rs10982455	0.83[EUR][1000 genomes]
rs10982456	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1126711	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12337739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12338765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347977	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12352646	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322058	0.82[GIH][hapmap];0.84[EUR][1000 genomes]
rs1322060	0.85[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1322067	0.97[EUR][1000 genomes]
rs1407309	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17292087	0.81[GIH][hapmap];0.84[EUR][1000 genomes]
rs2075533	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181036	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2208640	0.83[EUR][1000 genomes]
rs2295800	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2418324	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2418325	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2974	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181195	0.84[EUR][1000 genomes]
rs3181197	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181200	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181201	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181202	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3181348	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3181363	0.82[EUR][1000 genomes]
rs3181364	0.83[EUR][1000 genomes]
rs3181365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181366	0.83[EUR][1000 genomes]
rs3181367	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181368	0.83[EUR][1000 genomes]
rs3181369	0.83[EUR][1000 genomes]
rs3181370	0.83[EUR][1000 genomes]
rs3181371	0.83[EUR][1000 genomes]
rs3181372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181374	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4978611	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979470	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4979471	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979472	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979473	0.85[EUR][1000 genomes]
rs6478117	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025577	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7028578	0.84[EUR][1000 genomes]
rs7030090	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7032773	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7036962	0.83[EUR][1000 genomes]
rs7037640	0.85[EUR][1000 genomes]
rs726657	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7858603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872878	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs911603	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs927373	0.83[EUR][1000 genomes]
rs927374	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927375	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3789879	KIAA1958	cis	parietal	SCAN
rs3789879	ASTN2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:117670800-117687200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:117672400-117681600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr9:117672800-117682000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:117672800-117682600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr9:117673200-117683000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:117673200-117692400	Weak transcription	Spleen	Spleen
8	chr9:117673400-117678800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:117674800-117681000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:117675000-117680800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:117675200-117678600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr9:117675200-117679800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr9:117675400-117679600	Enhancers	Fetal Lung	lung
14	chr9:117675400-117680400	Strong transcription	Primary B cells from cord blood	blood
15	chr9:117676000-117678600	Weak transcription	Fetal Thymus	thymus
16	chr9:117676000-117688000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:117676600-117680400	Strong transcription	Thymus	Thymus
18	chr9:117677400-117679200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:117677600-117678600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:117677600-117680400	Strong transcription	Dnd41	blood
21	chr9:117677600-117680600	Strong transcription	Primary T cells from cord blood	blood
22	chr9:117677600-117684400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:117677800-117680600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:117678000-117678400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr9:117678000-117678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:117678000-117678800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:117678000-117678800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:117678000-117679000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:117678000-117680800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:117678000-117681200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:117678000-117687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:117678200-117680200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:117678200-117680400	Strong transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links