Variant report

Variant	rs1332598
Chromosome Location	chr9:103278418-103278419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1000477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1041565	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10465119	1.00[ASN][1000 genomes]
rs10465147	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10465148	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10465149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10512271	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10819773	1.00[JPT][hapmap]
rs10819774	0.81[CHB][hapmap]
rs10819776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10819782	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10819785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10819787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10819788	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10819789	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10819790	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	1.00[JPT][hapmap]
rs10989082	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10989085	1.00[JPT][hapmap]
rs10989094	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10989097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989105	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989120	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]
rs10989121	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10989123	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]
rs10989124	0.90[ASN][1000 genomes]
rs10989127	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10989134	0.89[ASN][1000 genomes]
rs10989135	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10989140	0.97[ASN][1000 genomes]
rs10989142	0.89[ASN][1000 genomes]
rs10989143	0.89[ASN][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10989146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989150	0.94[CHB][hapmap];0.82[JPT][hapmap];0.99[ASN][1000 genomes]
rs10989151	0.88[ASN][1000 genomes]
rs10989152	0.87[CHB][hapmap];0.92[ASN][1000 genomes]
rs10989153	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs10989154	0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[ASN][1000 genomes]
rs10989156	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs10989161	0.82[JPT][hapmap]
rs10989162	0.82[JPT][hapmap]
rs10989163	0.82[JPT][hapmap]
rs10989164	0.82[JPT][hapmap]
rs10989165	0.82[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]
rs12004257	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12235981	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12236970	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12683889	0.82[JPT][hapmap]
rs12684438	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12684454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs17741842	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17813663	0.80[MEX][hapmap]
rs17813801	0.80[MEX][hapmap]
rs17814768	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17814828	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1930237	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1930238	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1930246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1931140	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs2026423	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2026998	0.80[MEX][hapmap]
rs2069236	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2151106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2183989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2183990	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2183991	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2274882	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34471402	0.80[AMR][1000 genomes]
rs34816846	0.89[ASN][1000 genomes]
rs55827987	0.92[ASN][1000 genomes]
rs56163523	0.92[ASN][1000 genomes]
rs59565932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59823190	0.92[ASN][1000 genomes]
rs7021028	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs7028822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7029001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7031884	0.90[JPT][hapmap]
rs7038306	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7041189	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7042669	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7046659	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs72735148	0.88[ASN][1000 genomes]
rs72735154	1.00[ASN][1000 genomes]
rs7850353	0.88[ASN][1000 genomes]
rs7862727	0.81[AMR][1000 genomes]
rs7865385	0.86[MEX][hapmap];0.82[TSI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1332598	C9orf21	cis	cerebellum	SCAN
rs1332598	C9orf30	Cis_1M	lymphoblastoid	RTeQTL
rs1332598	C9orf30	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
3	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:103260800-103287200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:103261200-103287600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
8	chr9:103263200-103312200	Weak transcription	Fetal Kidney	kidney
9	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
10	chr9:103265400-103279800	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:103269400-103287000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:103270000-103289200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:103270200-103287200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:103270400-103283000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:103270800-103290000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:103272200-103279800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:103272600-103307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:103272800-103283600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:103272800-103285400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:103273000-103285200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:103273000-103303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:103273200-103283800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:103273400-103282200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:103273400-103289400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:103273600-103279400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:103273600-103287200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
28	chr9:103273800-103283600	Weak transcription	Fetal Brain Female	brain
29	chr9:103273800-103287200	Weak transcription	Brain Germinal Matrix	brain
30	chr9:103274400-103289400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:103276600-103278600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:103276800-103278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:103277600-103279000	Enhancers	HepG2	liver
34	chr9:103277800-103279000	Enhancers	Ovary	ovary
35	chr9:103278000-103279000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:103278000-103287800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:103278200-103278800	Weak transcription	Placenta	Placenta
38	chr9:103278200-103279000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:103278200-103289600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr9:103278400-103278800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:103278400-103279000	Enhancers	A549	lung
42	chr9:103278400-103279000	Enhancers	Hela-S3	cervix
43	chr9:103278400-103281400	Weak transcription	NHLF	lung
44	chr9:103278400-103286000	Weak transcription	Fetal Lung	lung
45	chr9:103278400-103288200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr9:103278400-103306400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:103278400-103333000	Weak transcription	Fetal Brain Male	brain

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