Variant report

Variant	rs2274882
Chromosome Location	chr9:103312290-103312291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1000477	0.80[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1041565	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10465118	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10465119	0.88[ASN][1000 genomes]
rs10465147	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10465148	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10465149	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10512270	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10512271	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10819773	1.00[JPT][hapmap]
rs10819776	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10819779	0.80[ASN][1000 genomes]
rs10819781	0.82[ASN][1000 genomes]
rs10819782	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10819785	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10819786	0.85[ASN][1000 genomes]
rs10819787	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10819788	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];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10819789	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10819790	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	1.00[JPT][hapmap]
rs10989082	0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10989085	1.00[JPT][hapmap]
rs10989094	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10989097	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10989099	0.82[ASN][1000 genomes]
rs10989103	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989108	0.85[ASN][1000 genomes]
rs10989111	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989112	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989113	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989114	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989115	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10989120	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]
rs10989121	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10989123	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]
rs10989124	0.98[ASN][1000 genomes]
rs10989127	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];0.95[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10989130	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10989131	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989134	0.97[ASN][1000 genomes]
rs10989135	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989140	0.85[ASN][1000 genomes]
rs10989142	0.97[ASN][1000 genomes]
rs10989143	0.97[ASN][1000 genomes]
rs10989144	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989145	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989146	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10989147	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10989150	0.88[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989151	0.98[ASN][1000 genomes]
rs10989152	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs10989153	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs10989154	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs10989156	1.00[CHB][hapmap];0.84[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	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12003523	0.80[EUR][1000 genomes]
rs12004257	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12056981	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12057047	0.85[ASN][1000 genomes]
rs12235981	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12236071	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12236952	0.85[ASN][1000 genomes]
rs12236970	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs12237166	0.82[ASN][1000 genomes]
rs12237481	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12238560	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12682741	0.82[ASN][1000 genomes]
rs12683122	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12683548	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12683889	0.82[JPT][hapmap]
rs12684438	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12684454	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13286805	0.85[ASN][1000 genomes]
rs13292589	0.85[ASN][1000 genomes]
rs1332598	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]
rs16919136	0.85[ASN][1000 genomes]
rs16919174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1930238	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs1930245	0.82[ASN][1000 genomes]
rs1930246	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1931140	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2026423	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2026998	0.80[MEX][hapmap]
rs2069236	0.80[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2151106	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2183989	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2183990	1.00[JPT][hapmap]
rs2183991	1.00[JPT][hapmap]
rs2274881	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34471402	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34816846	0.81[ASN][1000 genomes]
rs55827987	0.84[ASN][1000 genomes]
rs56163523	0.84[ASN][1000 genomes]
rs56170030	0.85[ASN][1000 genomes]
rs59565932	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59611728	0.84[ASN][1000 genomes]
rs59823190	0.84[ASN][1000 genomes]
rs7021028	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs7024666	0.82[ASN][1000 genomes]
rs7028822	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7029001	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7031884	0.90[JPT][hapmap]
rs7034154	0.82[ASN][1000 genomes]
rs7038306	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7041189	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7041933	0.82[ASN][1000 genomes]
rs7042669	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7046659	0.80[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs7049241	0.85[ASN][1000 genomes]
rs72735119	0.80[ASN][1000 genomes]
rs72735140	0.85[ASN][1000 genomes]
rs72735154	0.88[ASN][1000 genomes]
rs7850353	0.82[ASN][1000 genomes]
rs7862727	0.81[AMR][1000 genomes]
rs7865385	0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7869933	0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2274882	C9orf30	cis	lymphoblastoid	seeQTL
rs2274882	C9orf21	cis	cerebellum	SCAN
rs2274882	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
2	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
3	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
4	chr9:103278400-103333000	Weak transcription	Fetal Brain Male	brain
5	chr9:103296800-103316600	Weak transcription	HSMMtube	muscle
6	chr9:103297000-103312800	Weak transcription	Brain Anterior Caudate	brain
7	chr9:103300200-103327400	Weak transcription	Ovary	ovary
8	chr9:103300800-103319800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:103302400-103313000	Weak transcription	Fetal Lung	lung
10	chr9:103307400-103313000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:103307400-103316200	Weak transcription	Brain Substantia Nigra	brain
12	chr9:103307400-103316600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:103307400-103316600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:103307400-103317400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:103307400-103323600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:103307400-103331800	Weak transcription	Gastric	stomach
17	chr9:103307400-103332200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:103307600-103313200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:103307600-103320600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:103307800-103312400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:103307800-103312600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:103307800-103313600	Weak transcription	Fetal Stomach	stomach
25	chr9:103308000-103319400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:103308000-103321400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:103308000-103321600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:103308000-103327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:103308000-103340200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:103309200-103317800	Weak transcription	NH-A	brain
32	chr9:103309400-103318000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr9:103309800-103317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:103310000-103320600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:103310600-103312400	Enhancers	HUVEC	blood vessel
36	chr9:103311000-103313000	Strong transcription	Brain Germinal Matrix	brain
37	chr9:103311000-103313200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:103311000-103314400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:103311000-103316800	Strong transcription	Fetal Brain Female	brain
40	chr9:103311000-103328400	Weak transcription	Fetal Heart	heart
41	chr9:103311600-103316400	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:103311600-103330400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr9:103311800-103319600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:103311800-103321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr9:103312000-103313000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:103312000-103313400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:103312000-103313800	Strong transcription	HSMM	muscle
49	chr9:103312000-103316600	Weak transcription	Brain Angular Gyrus	brain
50	chr9:103312000-103319600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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