Variant report

Variant	rs10739236
Chromosome Location	chr9:110049848-110049849
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	chr9:110049581..110051989-chr9:110070046..110072937,2	MCF-7	breast:
2	chr9:110049612..110053509-chr9:110059334..110062914,3	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10113916	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10119641	0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs10122970	0.89[ASN][1000 genomes]
rs10481632	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10521083	0.88[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10739234	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10739238	0.92[AFR][1000 genomes]
rs10759222	0.85[CHD][hapmap]
rs10759225	0.80[CHD][hapmap]
rs10816477	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816480	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10816485	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816491	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10816498	1.00[YRI][hapmap]
rs10978767	0.83[CHB][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs10978775	0.85[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10978776	0.89[ASN][1000 genomes]
rs10978777	0.89[ASN][1000 genomes]
rs10978791	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12342066	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12345455	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs12551936	0.84[CEU][hapmap]
rs12555417	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1323809	0.80[CHD][hapmap]
rs1535765	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1805329	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805332	0.88[CHD][hapmap]
rs1805334	0.88[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs1805335	0.82[CHD][hapmap]
rs1886134	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1969798	0.80[AFR][1000 genomes]
rs1980725	0.80[AFR][1000 genomes]
rs2005143	0.84[ASN][1000 genomes]
rs2147071	0.85[AFR][1000 genomes]
rs2147072	0.85[CHD][hapmap]
rs2417776	0.89[ASN][1000 genomes]
rs2417784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28534368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28769087	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28848858	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4278207	0.88[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4625087	0.84[AFR][1000 genomes]
rs4978404	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4978406	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4978849	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs61701375	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698475	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7025563	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7029997	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7030169	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7030555	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7030631	0.85[AFR][1000 genomes]
rs7031906	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7035611	0.88[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7036284	0.89[ASN][1000 genomes]
rs7038737	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7039041	0.92[AFR][1000 genomes]
rs7040217	0.98[ASN][1000 genomes]
rs7041137	0.88[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs7041497	0.87[CHD][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7043962	0.86[AFR][1000 genomes]
rs7046950	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7856227	0.92[AFR][1000 genomes]
rs7867544	0.83[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs7873745	0.88[ASN][1000 genomes]
rs817836	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs817838	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817839	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817840	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817841	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817843	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817844	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817845	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817846	0.88[AFR][1000 genomes]
rs817847	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs817849	0.82[ASN][1000 genomes]
rs817851	0.82[ASN][1000 genomes]
rs942291	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs942292	0.85[CHD][hapmap]
rs942293	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9632893	0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969728	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10739236	OR13C8	cis	cerebellum	SCAN
rs10739236	TXN	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110045000-110050600	Active TSS	NHLF	lung
2	chr9:110046800-110050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:110046800-110050800	Weak transcription	Gastric	stomach
4	chr9:110046800-110050800	Weak transcription	Pancreas	Pancrea
5	chr9:110046800-110051000	Weak transcription	Spleen	Spleen
6	chr9:110047200-110050600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr9:110047200-110050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:110047200-110052400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:110047200-110052600	Enhancers	Primary B cells from peripheral blood	blood
10	chr9:110047200-110054600	Weak transcription	Lung	lung
11	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:110047800-110051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:110047800-110054200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr9:110048000-110050200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:110048000-110051000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:110048000-110051200	Enhancers	Thymus	Thymus
17	chr9:110048000-110053200	Weak transcription	Fetal Thymus	thymus
18	chr9:110048000-110056000	Weak transcription	Aorta	Aorta
19	chr9:110048000-110058400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:110048200-110050200	Enhancers	Fetal Heart	heart
21	chr9:110048400-110051200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:110048400-110051400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:110048400-110051800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr9:110048400-110052800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr9:110048400-110058000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr9:110048600-110050000	Enhancers	Colon Smooth Muscle	Colon
27	chr9:110048600-110050000	Enhancers	Left Ventricle	heart
28	chr9:110048600-110050400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:110048600-110050400	Weak transcription	Small Intestine	intestine
30	chr9:110048600-110050600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:110048600-110050800	Weak transcription	Ovary	ovary
32	chr9:110048600-110050800	Weak transcription	Right Atrium	heart
33	chr9:110048600-110051400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:110048600-110051600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:110048600-110052000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:110048600-110052000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:110048600-110052000	Active TSS	GM12878-XiMat	blood
38	chr9:110048600-110052200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr9:110048600-110058000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr9:110048800-110050000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:110048800-110050200	Weak transcription	HUVEC	blood vessel
42	chr9:110048800-110050400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr9:110048800-110051400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr9:110048800-110051400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:110048800-110051800	Weak transcription	Brain Substantia Nigra	brain
46	chr9:110048800-110051800	Weak transcription	Fetal Lung	lung
47	chr9:110048800-110052000	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:110048800-110052000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:110048800-110052200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:110048800-110052600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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