Variant report

Variant	rs2165715
Chromosome Location	chr9:97617034-97617035
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	chr9:97577340..97579614-chr9:97615490..97617196,2	MCF-7	breast:
2	chr9:97609417..97611385-chr9:97614090..97618041,3	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10122127	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10217441	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10732405	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10732407	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10733756	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739986	0.93[AFR][1000 genomes]
rs10739988	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739990	0.85[EUR][1000 genomes]
rs10761360	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761362	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs10761363	0.85[EUR][1000 genomes]
rs10821405	0.89[AFR][1000 genomes]
rs10821407	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821411	0.85[EUR][1000 genomes]
rs10993348	0.85[AFR][1000 genomes]
rs10993386	0.85[EUR][1000 genomes]
rs12344157	0.83[MKK][hapmap]
rs12553916	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12554043	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12555128	1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs1530331	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1542107	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs1542108	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs16911713	0.83[MKK][hapmap]
rs17355875	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs181488	0.85[AFR][1000 genomes]
rs191654	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2026399	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2095069	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2099868	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304884	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2406898	0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2406899	0.94[AFR][1000 genomes]
rs242260	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2584804	0.90[AFR][1000 genomes]
rs2584805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675168	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs356125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356132	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356135	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs356136	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356139	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356142	0.85[AFR][1000 genomes]
rs356145	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356147	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs356149	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs365465	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs367319	1.00[EUR][1000 genomes]
rs376902	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs384039	0.85[AFR][1000 genomes]
rs3886568	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3887267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3910730	0.82[EUR][1000 genomes]
rs397783	0.87[AMR][1000 genomes]
rs397806	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs415016	0.92[AFR][1000 genomes]
rs422502	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4332191	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs438742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448899	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs456276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs457795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4612413	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743968	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743970	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743972	0.82[EUR][1000 genomes]
rs4743973	0.82[EUR][1000 genomes]
rs4744379	0.82[AFR][1000 genomes]
rs4744380	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4744382	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744383	0.91[AFR][1000 genomes]
rs4744387	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744388	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555799	0.97[EUR][1000 genomes]
rs56198429	0.94[EUR][1000 genomes]
rs562605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56317174	0.94[EUR][1000 genomes]
rs58281499	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61086657	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479570	0.91[AFR][1000 genomes]
rs6479571	0.91[AFR][1000 genomes]
rs6479572	0.92[AFR][1000 genomes]
rs6479574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs6479575	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479576	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479577	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479579	0.85[EUR][1000 genomes]
rs6479581	0.85[EUR][1000 genomes]
rs6479582	0.85[EUR][1000 genomes]
rs6479583	0.85[EUR][1000 genomes]
rs66495734	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66710673	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67208365	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68090960	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68091393	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7019602	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7022963	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7025100	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7025934	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7026714	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7029570	1.00[MEX][hapmap]
rs7031172	0.85[LWK][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs7035166	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7038519	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7038891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044371	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045387	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7047478	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72747019	0.94[EUR][1000 genomes]
rs7341710	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7855781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864389	0.89[AMR][1000 genomes]
rs7867856	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7869666	1.00[YRI][hapmap]
rs7869736	0.85[TSI][hapmap]
rs7870679	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs894425	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs894426	0.85[EUR][1000 genomes]
rs894428	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9409589	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9409805	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2165715	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97571800-97622600	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97589200-97622400	Weak transcription	Aorta	Aorta
3	chr9:97602400-97620200	Weak transcription	GM12878-XiMat	blood
4	chr9:97602400-97622200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97603200-97624600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:97605600-97622600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:97605800-97621800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:97605800-97626000	Weak transcription	Right Atrium	heart
9	chr9:97609800-97618400	Weak transcription	Lung	lung
10	chr9:97609800-97620600	Weak transcription	Fetal Stomach	stomach
11	chr9:97609800-97623800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:97610200-97623200	Weak transcription	Fetal Intestine Large	intestine
13	chr9:97610200-97625800	Weak transcription	Right Ventricle	heart
14	chr9:97610400-97620400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:97610400-97622400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:97610400-97623600	Weak transcription	Fetal Kidney	kidney
17	chr9:97610600-97620400	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:97610600-97622200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:97610600-97623000	Weak transcription	NHLF	lung
20	chr9:97611200-97622600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:97611400-97620800	Weak transcription	Placenta	Placenta
22	chr9:97612000-97627600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:97612800-97626200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:97613800-97617200	Enhancers	HepG2	liver
25	chr9:97614000-97627800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:97614800-97622400	Weak transcription	Primary T cells from cord blood	blood
27	chr9:97614800-97623400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:97614800-97623400	Weak transcription	Esophagus	oesophagus
29	chr9:97615000-97618200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:97615000-97620600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:97615000-97620600	Weak transcription	Thymus	Thymus
32	chr9:97615000-97622600	Weak transcription	HSMMtube	muscle
33	chr9:97615000-97622800	Weak transcription	NHDF-Ad	bronchial
34	chr9:97615000-97623200	Weak transcription	Pancreas	Pancrea
35	chr9:97615000-97623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:97616200-97617400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr9:97616200-97623600	Weak transcription	Fetal Lung	lung
38	chr9:97616400-97618000	Weak transcription	NHEK	skin
39	chr9:97616400-97618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:97616400-97620600	Weak transcription	Fetal Intestine Small	intestine
41	chr9:97616400-97622600	Weak transcription	Osteobl	bone
42	chr9:97616400-97623200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:97616400-97623400	Weak transcription	Brain Angular Gyrus	brain
44	chr9:97616600-97618000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:97616600-97618200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:97616600-97621400	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:97616600-97629600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:97616800-97622600	Weak transcription	NH-A	brain
49	chr9:97616800-97623200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:97616800-97623400	Weak transcription	Stomach Mucosa	stomach

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