Variant report

Variant	rs10989120
Chromosome Location	chr9:103263814-103263815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1000477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1041565	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs10465145	0.88[ASN][1000 genomes]
rs10465147	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs10465148	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap]
rs10465149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs10512271	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10819774	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs10819775	0.88[ASN][1000 genomes]
rs10819776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs10819779	0.95[ASN][1000 genomes]
rs10819781	0.97[ASN][1000 genomes]
rs10819782	1.00[CHB][hapmap];0.83[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819785	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10819786	1.00[ASN][1000 genomes]
rs10819787	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10819788	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819789	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10819790	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10989078	0.81[JPT][hapmap]
rs10989082	0.87[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs10989085	0.83[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[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs10989095	0.95[ASN][1000 genomes]
rs10989097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989099	0.97[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989105	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989108	1.00[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989121	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989123	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]
rs10989124	0.87[ASN][1000 genomes]
rs10989127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10989130	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989134	0.86[ASN][1000 genomes]
rs10989135	0.93[AMR][1000 genomes];0.92[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[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989146	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs10989150	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs10989151	0.85[ASN][1000 genomes]
rs10989152	0.86[CHB][hapmap]
rs10989153	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap]
rs10989154	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs10989156	0.94[CHB][hapmap]
rs10989161	0.83[JPT][hapmap]
rs10989162	0.83[JPT][hapmap]
rs10989163	0.81[JPT][hapmap]
rs10989164	0.81[JPT][hapmap]
rs10989165	0.83[JPT][hapmap]
rs10989167	0.81[JPT][hapmap]
rs10989169	0.81[JPT][hapmap]
rs10989170	0.81[JPT][hapmap]
rs11793014	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs12004257	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005378	0.84[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs12057047	1.00[ASN][1000 genomes]
rs12235981	0.93[CHB][hapmap]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs12236952	1.00[ASN][1000 genomes]
rs12236970	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs12237166	0.97[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs12682741	0.97[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs12683889	0.81[JPT][hapmap]
rs12684438	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs12684454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13286805	1.00[ASN][1000 genomes]
rs13292589	1.00[ASN][1000 genomes]
rs1332598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919136	1.00[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs16919204	0.83[JPT][hapmap]
rs16919211	0.83[JPT][hapmap]
rs17741842	0.82[TSI][hapmap]
rs17814768	0.82[TSI][hapmap]
rs17814828	0.81[TSI][hapmap]
rs1930237	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1930238	0.82[TSI][hapmap]
rs1930245	0.97[ASN][1000 genomes]
rs1930246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs1931140	0.94[CHB][hapmap]
rs2026423	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2069236	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2151106	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2183989	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2183990	0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2183991	0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs2274882	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34471402	0.80[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	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59611728	0.99[ASN][1000 genomes]
rs7021028	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap]
rs7024666	0.97[ASN][1000 genomes]
rs7028822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7029001	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7034154	0.97[ASN][1000 genomes]
rs7041189	0.82[TSI][hapmap]
rs7041933	0.97[ASN][1000 genomes]
rs7042669	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs7046659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[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]
rs7865385	0.82[TSI][hapmap]
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
rs10989120	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103238200-103264200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:103238200-103274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:103255200-103271000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:103255400-103277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:103255600-103265800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:103255600-103266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:103255600-103272400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:103255600-103272400	Weak transcription	Fetal Brain Female	brain
9	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:103255800-103266000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:103255800-103272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:103256200-103265000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
14	chr9:103256400-103271600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:103257000-103272400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:103260400-103264800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:103260400-103272200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:103260400-103272200	Weak transcription	Brain Substantia Nigra	brain
21	chr9:103260800-103287200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:103261000-103265600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:103261000-103272400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:103261200-103264000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:103261200-103267200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:103261200-103287600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
28	chr9:103262600-103272400	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:103263200-103267200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:103263200-103312200	Weak transcription	Fetal Kidney	kidney
31	chr9:103263400-103265800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:103263400-103273800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:103263400-103278200	Weak transcription	Fetal Lung	lung
34	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
35	chr9:103263600-103264200	Strong transcription	Brain Germinal Matrix	brain
36	chr9:103263600-103265000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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