Variant report

Variant	rs10989123
Chromosome Location	chr9:103272330-103272331
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1000477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1041565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10465145	0.88[ASN][1000 genomes]
rs10465147	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10465148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10465149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10512270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10512271	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10819773	0.90[JPT][hapmap]
rs10819774	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs10819775	0.88[ASN][1000 genomes]
rs10819776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10819779	0.95[ASN][1000 genomes]
rs10819781	0.97[ASN][1000 genomes]
rs10819782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10819786	1.00[ASN][1000 genomes]
rs10819787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10819788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10819790	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	0.91[JPT][hapmap]
rs10989082	1.00[JPT][hapmap]
rs10989085	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10989090	0.91[ASN][1000 genomes]
rs10989091	0.93[ASN][1000 genomes]
rs10989092	0.95[ASN][1000 genomes]
rs10989093	0.91[ASN][1000 genomes]
rs10989094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10989095	0.95[ASN][1000 genomes]
rs10989097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989099	0.97[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989105	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989108	1.00[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989121	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989124	0.87[ASN][1000 genomes]
rs10989127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10989130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989134	0.86[ASN][1000 genomes]
rs10989135	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10989142	0.86[ASN][1000 genomes]
rs10989143	0.86[ASN][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989147	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989150	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10989151	0.85[ASN][1000 genomes]
rs10989152	0.88[CHB][hapmap]
rs10989153	0.94[CHB][hapmap]
rs10989154	0.94[CHB][hapmap]
rs10989156	0.94[CHB][hapmap]
rs10989161	0.84[JPT][hapmap]
rs10989162	0.84[JPT][hapmap]
rs10989163	0.82[JPT][hapmap]
rs10989164	0.82[JPT][hapmap]
rs10989165	0.84[JPT][hapmap]
rs10989167	0.82[JPT][hapmap]
rs10989169	0.82[JPT][hapmap]
rs10989170	0.82[JPT][hapmap]
rs11793014	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12004257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005378	0.84[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12057047	1.00[ASN][1000 genomes]
rs12235981	0.94[CHB][hapmap]
rs12236071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12236952	1.00[ASN][1000 genomes]
rs12236970	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs12237166	0.97[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12682741	0.97[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12683889	0.82[JPT][hapmap]
rs12684438	1.00[JPT][hapmap]
rs12684454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13286805	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13292589	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1332598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16919136	1.00[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16919204	0.83[JPT][hapmap]
rs16919211	0.84[JPT][hapmap]
rs1930237	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1930245	0.97[ASN][1000 genomes]
rs1930246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1931140	0.94[CHB][hapmap]
rs2026423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2069236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2151106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2183989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2183990	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2183991	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2274881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2274882	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34471402	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56050588	0.82[ASN][1000 genomes]
rs56122790	0.88[ASN][1000 genomes]
rs56170030	1.00[ASN][1000 genomes]
rs59565932	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59611728	0.99[ASN][1000 genomes]
rs7021028	0.94[CHB][hapmap]
rs7024666	0.97[ASN][1000 genomes]
rs7028822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7029001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7031884	0.82[JPT][hapmap]
rs7034154	0.97[ASN][1000 genomes]
rs7038306	0.80[AMR][1000 genomes]
rs7041933	0.97[ASN][1000 genomes]
rs7042669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7046659	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7049241	1.00[ASN][1000 genomes]
rs72735107	0.88[ASN][1000 genomes]
rs72735110	0.88[ASN][1000 genomes]
rs72735119	0.95[ASN][1000 genomes]
rs72735122	0.95[ASN][1000 genomes]
rs72735140	1.00[ASN][1000 genomes]
rs72735148	0.90[ASN][1000 genomes]
rs7869933	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10989123	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103238200-103274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:103255400-103277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:103255600-103272400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:103255600-103272400	Weak transcription	Fetal Brain Female	brain
5	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:103255800-103272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
8	chr9:103257000-103272400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
11	chr9:103260800-103287200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:103261000-103272400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:103261200-103287600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
15	chr9:103262600-103272400	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:103263200-103312200	Weak transcription	Fetal Kidney	kidney
17	chr9:103263400-103273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:103263400-103278200	Weak transcription	Fetal Lung	lung
19	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
20	chr9:103264800-103277000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:103265200-103277800	Weak transcription	Ovary	ovary
22	chr9:103265400-103272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:103265400-103279800	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:103265600-103272400	Weak transcription	Brain Angular Gyrus	brain
25	chr9:103269400-103287000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:103270000-103289200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:103270200-103287200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:103270400-103283000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:103270600-103273600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:103270600-103274000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:103270600-103276600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:103270800-103290000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:103271200-103273000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:103271200-103273200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr9:103271400-103272400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:103271400-103273000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:103271400-103273800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:103271600-103273400	Weak transcription	Brain Germinal Matrix	brain
39	chr9:103271600-103278000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:103271800-103272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr9:103271800-103272400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr9:103272000-103274200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:103272200-103273200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:103272200-103279800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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