Variant report

Variant	rs1322058
Chromosome Location	chr9:117684547-117684548
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	chr9:117683235..117685068-chr9:117691767..117694448,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106952	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1006025	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006026	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006027	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10081728	0.96[ASN][1000 genomes]
rs10817682	0.83[EUR][1000 genomes]
rs10817683	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817684	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817685	0.86[ASN][1000 genomes]
rs10982445	0.81[EUR][1000 genomes]
rs10982449	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982450	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982451	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982455	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982456	0.83[EUR][1000 genomes]
rs1126711	0.83[EUR][1000 genomes]
rs12337739	0.83[EUR][1000 genomes]
rs12338765	0.84[EUR][1000 genomes]
rs12347977	0.84[EUR][1000 genomes]
rs12352646	0.83[EUR][1000 genomes]
rs1322054	0.82[EUR][1000 genomes]
rs1322056	0.83[EUR][1000 genomes]
rs1322059	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322060	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1322067	0.83[EUR][1000 genomes]
rs1555456	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555457	0.83[ASN][1000 genomes]
rs17292087	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075534	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181033	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181036	0.81[EUR][1000 genomes]
rs2208640	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295800	0.83[EUR][1000 genomes]
rs2974	0.82[EUR][1000 genomes]
rs3181195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181197	0.82[EUR][1000 genomes]
rs3181200	0.83[EUR][1000 genomes]
rs3181201	0.83[EUR][1000 genomes]
rs3181202	0.83[EUR][1000 genomes]
rs3181363	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181364	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181365	0.82[EUR][1000 genomes]
rs3181366	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181367	0.82[EUR][1000 genomes]
rs3181368	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181369	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181370	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181371	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3181372	0.82[EUR][1000 genomes]
rs3181374	0.83[EUR][1000 genomes]
rs3789879	0.84[EUR][1000 genomes]
rs4978611	0.84[EUR][1000 genomes]
rs4979470	0.80[EUR][1000 genomes]
rs4979471	0.81[EUR][1000 genomes]
rs4979472	0.84[EUR][1000 genomes]
rs4979473	0.96[ASN][1000 genomes]
rs6478117	0.82[EUR][1000 genomes]
rs7025577	0.81[EUR][1000 genomes]
rs7028578	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7030090	0.83[EUR][1000 genomes]
rs7032773	0.80[EUR][1000 genomes]
rs7036962	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037640	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726656	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726657	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7858603	0.83[EUR][1000 genomes]
rs7872878	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927373	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927374	0.84[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1322058	ASTN2	cis	cerebellum	SCAN
rs1322058	KIAA1958	cis	parietal	SCAN
rs1322058	SNORA70C	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117670800-117687200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:117673200-117692400	Weak transcription	Spleen	Spleen
3	chr9:117676000-117688000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:117678000-117687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:117679600-117687000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:117680200-117690400	Weak transcription	Fetal Thymus	thymus
7	chr9:117680600-117688400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:117680800-117689600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr9:117681200-117688200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:117682000-117685600	Genic enhancers	Thymus	Thymus
11	chr9:117682000-117689600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr9:117682400-117687200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr9:117682400-117689800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:117682600-117686200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr9:117682600-117687000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:117682600-117688200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr9:117682600-117688200	Weak transcription	Fetal Lung	lung
18	chr9:117683200-117685200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr9:117683200-117689000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:117683400-117688600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
21	chr9:117683600-117684800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:117683600-117685000	Genic enhancers	Primary T cells from cord blood	blood
23	chr9:117683800-117684600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:117684000-117687000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr9:117684200-117684800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr9:117684200-117687000	Weak transcription	Dnd41	blood
27	chr9:117684400-117684600	Strong transcription	Primary B cells from cord blood	blood
28	chr9:117684400-117684600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:117684400-117684800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr9:117684400-117685200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:117684400-117685600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:117684400-117689600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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