Variant report

Variant	rs603947
Chromosome Location	chr9:98706929-98706930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115110	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10117340	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10125109	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10512242	0.81[AMR][1000 genomes]
rs10512245	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739705	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760189	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760261	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760269	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760679	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818574	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10818899	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10819663	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819668	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985156	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10985499	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10987963	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989035	0.85[AMR][1000 genomes]
rs1195130	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11998982	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12345187	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12347675	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12348051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12349742	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1327996	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1327997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13289466	0.81[EUR][1000 genomes]
rs13294931	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026031	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296858	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2405134	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2405371	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2405372	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2943532	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs589362	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617187	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625105	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62559026	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62559767	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs640297	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478977	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs649819	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657451	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs666093	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs671058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs682682	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684455	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686048	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689619	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689696	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689697	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689738	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689744	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689761	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs689804	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs689860	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689911	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689986	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs690056	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690063	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690495	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690528	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs690633	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs694230	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs700962	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7847983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852346	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7871709	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816670	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816672	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816673	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816674	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816675	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816682	0.85[AMR][1000 genomes]
rs816683	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816684	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs603947	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs603947	C9orf102	cis	multi-tissue	Pritchard
rs603947	ERCC6L2	cis	Artery Tibial	GTEx
rs603947	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
3	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
4	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
7	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
8	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:98687800-98709000	Weak transcription	Lung	lung
11	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
12	chr9:98687800-98726000	Weak transcription	Gastric	stomach
13	chr9:98690400-98707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:98690600-98709800	Weak transcription	HMEC	breast
15	chr9:98694600-98708400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:98695600-98718200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:98695800-98709200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:98695800-98742400	Weak transcription	NHLF	lung
19	chr9:98696200-98709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:98697800-98707000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:98697800-98713200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:98698800-98709200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:98699200-98707000	Strong transcription	Fetal Thymus	thymus
24	chr9:98699400-98709000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:98699400-98709600	Weak transcription	Brain Substantia Nigra	brain
26	chr9:98699600-98708400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:98699600-98717600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:98699800-98718600	Weak transcription	NHEK	skin
29	chr9:98700600-98707000	Strong transcription	Liver	Liver
30	chr9:98701600-98709000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:98702000-98707000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:98702400-98707000	Strong transcription	Fetal Intestine Large	intestine
33	chr9:98702400-98709200	Weak transcription	Fetal Stomach	stomach
34	chr9:98702400-98718600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:98702400-98718600	Weak transcription	Small Intestine	intestine
36	chr9:98702600-98707000	Strong transcription	Primary B cells from cord blood	blood
37	chr9:98702600-98707800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr9:98702600-98708400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:98702600-98709000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:98702600-98709000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:98702600-98709400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:98702600-98718600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:98702600-98718600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:98702600-98718600	Weak transcription	Aorta	Aorta
45	chr9:98702600-98718600	Weak transcription	Pancreas	Pancrea
46	chr9:98703200-98707000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:98703600-98707000	Strong transcription	A549	lung
48	chr9:98703600-98709000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:98703600-98709400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:98704000-98707000	Strong transcription	Duodenum Mucosa	Duodenum

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