Variant report

Variant	rs12352646
Chromosome Location	chr9:117676518-117676519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117444446..117445144-chr9:117675660..117676526,3	MCF-7	breast:
2	chr9:117676223..117677155-chr9:117776236..117776995,3	MCF-7	breast:
3	chr9:117676108..117677078-chr9:117776037..117776911,10	MCF-7	breast:
4	chr9:117676278..117677112-chr9:117777453..117778259,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1006025	0.82[EUR][1000 genomes]
rs1006026	0.94[EUR][1000 genomes]
rs1006027	0.82[EUR][1000 genomes]
rs10081728	0.83[EUR][1000 genomes]
rs10817679	0.88[ASN][1000 genomes]
rs10817682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817683	0.95[EUR][1000 genomes]
rs10817685	0.81[EUR][1000 genomes]
rs10982445	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982449	0.83[EUR][1000 genomes]
rs10982450	0.84[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	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1126711	0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12337739	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12338765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322054	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322056	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1322058	0.83[EUR][1000 genomes]
rs1322060	0.82[EUR][1000 genomes]
rs1322067	0.96[EUR][1000 genomes]
rs1407309	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17292087	0.83[EUR][1000 genomes]
rs2075533	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181036	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2208640	0.84[EUR][1000 genomes]
rs2295800	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2418324	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2418325	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2974	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3181195	0.83[EUR][1000 genomes]
rs3181197	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181200	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181201	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181202	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181348	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3181363	0.82[EUR][1000 genomes]
rs3181364	0.84[EUR][1000 genomes]
rs3181365	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181366	0.84[EUR][1000 genomes]
rs3181367	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.82[EUR][1000 genomes]
rs3181372	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3181374	0.89[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3789879	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979470	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4979471	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979472	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979473	0.84[EUR][1000 genomes]
rs6478117	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025577	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7028578	0.84[EUR][1000 genomes]
rs7030090	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032773	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7036962	0.83[EUR][1000 genomes]
rs7037640	0.84[EUR][1000 genomes]
rs726657	0.84[EUR][1000 genomes]
rs7858603	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7872878	0.97[EUR][1000 genomes]
rs911603	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs927373	0.84[EUR][1000 genomes]
rs927374	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927375	0.90[AMR][1000 genomes];0.84[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

No data

Chromatin state (count:34 , 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	chr9:117671200-117676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:117671800-117676600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:117671800-117676800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:117672200-117676600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:117672400-117681600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:117672800-117682000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:117672800-117682600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:117673200-117676800	Strong transcription	Primary T cells from cord blood	blood
11	chr9:117673200-117677000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:117673200-117683000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:117673200-117692400	Weak transcription	Spleen	Spleen
14	chr9:117673400-117678800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:117673600-117676600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:117673600-117677000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:117674200-117676600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:117674400-117677600	Genic enhancers	Dnd41	blood
19	chr9:117674800-117676600	Genic enhancers	Thymus	Thymus
20	chr9:117674800-117681000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:117675000-117680800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:117675200-117677000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr9:117675200-117678600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr9:117675200-117679800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr9:117675400-117679600	Enhancers	Fetal Lung	lung
26	chr9:117675400-117680400	Strong transcription	Primary B cells from cord blood	blood
27	chr9:117675800-117677000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr9:117676000-117678000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr9:117676000-117678600	Weak transcription	Fetal Thymus	thymus
30	chr9:117676000-117688000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:117676400-117676800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:117676400-117676800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:117676400-117678000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:117676400-117678000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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