Variant report

Variant	rs1407309
Chromosome Location	chr9:117651780-117651781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1006026	0.91[EUR][1000 genomes]
rs10081728	0.83[EUR][1000 genomes]
rs10817682	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10817683	0.92[EUR][1000 genomes]
rs10982445	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10982450	0.81[EUR][1000 genomes]
rs10982451	0.80[EUR][1000 genomes]
rs10982456	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1126711	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12337739	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12338765	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12347977	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12352646	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1322054	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1322056	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1322058	0.82[CHD][hapmap]
rs1322060	0.89[CEU][hapmap];0.84[CHD][hapmap];0.83[TSI][hapmap]
rs1322067	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17292087	0.81[CHD][hapmap];0.82[EUR][1000 genomes]
rs2075533	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2181036	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208640	0.81[EUR][1000 genomes]
rs2295800	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2418324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418325	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181195	0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs3181197	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3181200	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181201	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181202	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181348	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3181363	0.80[EUR][1000 genomes]
rs3181364	0.81[EUR][1000 genomes]
rs3181365	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3181366	0.81[EUR][1000 genomes]
rs3181367	0.91[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3181368	0.81[EUR][1000 genomes]
rs3181369	0.81[CHD][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs3181370	0.81[EUR][1000 genomes]
rs3181371	0.81[EUR][1000 genomes]
rs3181372	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3181374	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789879	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4978611	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4979470	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979471	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4979472	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4979473	0.82[EUR][1000 genomes]
rs5003740	0.87[ASN][1000 genomes]
rs6478117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025577	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7028578	0.81[EUR][1000 genomes]
rs7030090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032773	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7037640	0.81[EUR][1000 genomes]
rs726657	0.92[CEU][hapmap];0.84[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7858603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7872878	0.93[EUR][1000 genomes]
rs911603	0.88[AMR][1000 genomes]
rs927373	0.81[EUR][1000 genomes]
rs927374	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs927375	0.88[AMR][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
rs1407309	ASTN2	cis	cerebellum	SCAN
rs1407309	KIAA1958	cis	parietal	SCAN
rs1407309	SNORA70C	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117643000-117652000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:117647400-117651800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:117647800-117651800	Weak transcription	Stomach Mucosa	stomach
4	chr9:117647800-117655600	Weak transcription	NHDF-Ad	bronchial
5	chr9:117649200-117652800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr9:117649400-117653400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:117649400-117653400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr9:117650200-117652600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr9:117650200-117653000	Enhancers	Primary T cells from cord blood	blood
10	chr9:117650400-117652400	Enhancers	Liver	Liver
11	chr9:117650400-117652800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:117650400-117652800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr9:117650400-117653000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:117650400-117653000	Enhancers	Dnd41	blood
15	chr9:117650600-117652800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr9:117650600-117653600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr9:117650800-117652400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr9:117650800-117652600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr9:117650800-117652800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr9:117650800-117652800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:117650800-117652800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr9:117650800-117652800	Enhancers	Fetal Thymus	thymus
23	chr9:117651000-117651800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr9:117651000-117652600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:117651000-117652600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:117651000-117652600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:117651000-117652800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:117651000-117652800	Enhancers	Thymus	Thymus
29	chr9:117651000-117653000	Enhancers	Primary B cells from peripheral blood	blood
30	chr9:117651000-117653200	Enhancers	Primary B cells from cord blood	blood
31	chr9:117651200-117652600	Enhancers	Spleen	Spleen
32	chr9:117651200-117652800	Enhancers	Hela-S3	cervix
33	chr9:117651200-117656000	Weak transcription	Adipose Nuclei	Adipose
34	chr9:117651200-117656000	Weak transcription	HepG2	liver
35	chr9:117651400-117651800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr9:117651400-117651800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117651400-117652400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:117651400-117652400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:117651400-117652600	Enhancers	Esophagus	oesophagus
40	chr9:117651400-117653000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:117651400-117655800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:117651400-117656200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:117651600-117652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:117651600-117652400	Enhancers	HMEC	breast
45	chr9:117651600-117652600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:117651600-117652600	Enhancers	Gastric	stomach
47	chr9:117651600-117652800	Enhancers	Primary hematopoietic stem cells	blood
48	chr9:117651600-117656600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:117651600-117656600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:117651600-117656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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