Variant report

Variant	rs2418326
Chromosome Location	chr9:117679474-117679475
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	chr9:117677998..117681403-chr9:117681907..117683952,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10982521	1.00[JPT][hapmap]
rs11793394	1.00[JPT][hapmap]
rs11795369	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12380758	1.00[JPT][hapmap]
rs1407308	1.00[JPT][hapmap]
rs1513	1.00[JPT][hapmap]
rs1885386	0.84[ASN][1000 genomes]
rs3181354	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4979465	0.84[ASN][1000 genomes]
rs4979474	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048073	0.84[ASN][1000 genomes]
rs726658	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7847158	1.00[JPT][hapmap];0.86[MKK][hapmap]
rs7874896	0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2418326	ASTN2	cis	cerebellum	SCAN
rs2418326	SNORA70C	cis	cerebellum	SCAN
rs2418326	KIAA1958	cis	parietal	SCAN

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	chr9:117672400-117681600	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	chr9:117674800-117681000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:117675000-117680800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr9:117675200-117679800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
11	chr9:117675400-117679600	Enhancers	Fetal Lung	lung
12	chr9:117675400-117680400	Strong transcription	Primary B cells from cord blood	blood
13	chr9:117676000-117688000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:117676600-117680400	Strong transcription	Thymus	Thymus
15	chr9:117677600-117680400	Strong transcription	Dnd41	blood
16	chr9:117677600-117680600	Strong transcription	Primary T cells from cord blood	blood
17	chr9:117677600-117684400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:117677800-117680600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:117678000-117680800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:117678000-117681200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:117678000-117687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:117678200-117680200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:117678200-117680400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:117678400-117680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:117678400-117680600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr9:117678600-117679600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr9:117678600-117679600	Enhancers	Fetal Stomach	stomach
28	chr9:117678600-117680200	Strong transcription	Fetal Thymus	thymus
29	chr9:117678600-117680400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr9:117678800-117679600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr9:117679000-117680400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:117679200-117680400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:117679200-117680600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr9:117679400-117681400	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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