Variant report

Variant	rs10989082
Chromosome Location	chr9:103174200-103174201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213031065..213031850-chr9:103173442..103174223,2	Hela-S3	cervix:
2	chr9:103162892..103165922-chr9:103171980..103175521,3	MCF-7	breast:
3	chr9:103171653..103179256-chr9:103186952..103193020,13	MCF-7	breast:
4	chr9:103169579..103171733-chr9:103173238..103174816,2	K562	blood:
5	chr9:103114138..103117790-chr9:103172786..103175922,6	MCF-7	breast:
6	chr9:103169516..103171661-chr9:103172507..103175663,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000136891	Chromatin interaction
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1000477	0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10465118	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10465147	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10465148	0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10465149	1.00[JPT][hapmap]
rs10512270	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10512271	1.00[JPT][hapmap]
rs10819773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819774	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10819776	1.00[ASW][hapmap];0.83[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10819782	1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs10819785	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10819787	1.00[JPT][hapmap]
rs10819788	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10819789	0.94[ASW][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10989078	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs10989081	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989085	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10989094	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs10989097	1.00[ASW][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs10989103	1.00[JPT][hapmap]
rs10989105	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10989107	1.00[JPT][hapmap]
rs10989111	1.00[JPT][hapmap]
rs10989112	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10989113	1.00[JPT][hapmap]
rs10989114	1.00[JPT][hapmap]
rs10989115	1.00[JPT][hapmap]
rs10989120	0.87[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs10989123	1.00[JPT][hapmap]
rs10989127	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10989130	1.00[JPT][hapmap]
rs10989131	1.00[JPT][hapmap]
rs10989144	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10989145	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10989146	1.00[JPT][hapmap]
rs10989147	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10989150	0.82[JPT][hapmap]
rs10989153	0.82[CHD][hapmap];0.80[GIH][hapmap]
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[JPT][hapmap];0.93[YRI][hapmap]
rs12004257	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12056981	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12236071	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12236970	0.82[CHD][hapmap]
rs12237481	1.00[JPT][hapmap]
rs12238560	1.00[JPT][hapmap]
rs1226588	0.82[YRI][hapmap]
rs1226594	0.85[YRI][hapmap]
rs12683122	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12683548	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12683889	0.82[JPT][hapmap]
rs12684438	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684454	1.00[JPT][hapmap]
rs1332598	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs16919174	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs1930245	0.81[EUR][1000 genomes]
rs1930246	0.94[ASW][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2026423	0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2069236	0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2151106	1.00[JPT][hapmap]
rs2183989	1.00[JPT][hapmap]
rs2183990	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2183991	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2274881	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2274882	0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2780959	0.85[YRI][hapmap]
rs7021028	0.80[GIH][hapmap]
rs7028822	0.94[ASW][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7029001	1.00[JPT][hapmap]
rs7031884	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7042669	1.00[JPT][hapmap]
rs7046596	0.98[ASN][1000 genomes]
rs7046659	0.82[ASW][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs72733399	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10989082	C9orf30	cis	lymphoblastoid	seeQTL
rs10989082	C9orf30	Cis_1M	lymphoblastoid	RTeQTL
rs10989082	CA11	trans	cerebellum	SCAN

Chromatin state (count:146 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103172400-103174600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr9:103173200-103174800	Active TSS	Rectal Smooth Muscle	rectum
3	chr9:103173400-103174200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:103173400-103174400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:103173400-103174400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:103173400-103174400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:103173400-103174400	Active TSS	Fetal Kidney	kidney
8	chr9:103173400-103174600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:103173400-103174600	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr9:103173400-103174600	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr9:103173400-103174600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr9:103173400-103174600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr9:103173400-103174600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:103173400-103174600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:103173400-103174600	Active TSS	Colonic Mucosa	Colon
16	chr9:103173400-103174600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr9:103173400-103174600	Active TSS	GM12878-XiMat	blood
18	chr9:103173400-103174600	Flanking Active TSS	NHEK	skin
19	chr9:103173400-103174800	Active TSS	Brain Angular Gyrus	brain
20	chr9:103173400-103174800	Active TSS	Brain Substantia Nigra	brain
21	chr9:103173600-103174200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:103173600-103174200	Active TSS	Fetal Brain Male	brain
23	chr9:103173600-103174200	Active TSS	Lung	lung
24	chr9:103173600-103174200	Active TSS	NH-A	brain
25	chr9:103173600-103174400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr9:103173600-103174400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:103173600-103174400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:103173600-103174400	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr9:103173600-103174400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:103173600-103174400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr9:103173600-103174400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr9:103173600-103174400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr9:103173600-103174400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:103173600-103174400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:103173600-103174400	Active TSS	Brain Anterior Caudate	brain
36	chr9:103173600-103174400	Flanking Active TSS	Placenta	Placenta
37	chr9:103173600-103174400	Active TSS	Placenta Amnion	Placenta Amnion
38	chr9:103173600-103174400	Active TSS	Thymus	Thymus
39	chr9:103173600-103174600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:103173600-103174600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:103173600-103174600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr9:103173600-103174600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr9:103173600-103174600	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr9:103173600-103174600	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr9:103173600-103174600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr9:103173600-103174600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr9:103173600-103174600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:103173600-103174600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:103173600-103174600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr9:103173600-103174600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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