Variant report

Variant	rs671058
Chromosome Location	chr9:98694010-98694011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98692437..98694773-chr9:98695538..98697868,2	K562	blood:
2	chr9:98692437..98694595-chr9:98695109..98697038,2	K562	blood:
3	chr9:98684128..98686659-chr9:98692175..98694024,2	K562	blood:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

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	0.95[CEU][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760189	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760261	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760269	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10760679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818574	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10818899	0.89[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10819650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819663	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819668	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10985156	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10985499	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10987963	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10989035	0.85[AMR][1000 genomes]
rs1195130	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11998982	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12345187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12347675	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12348051	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349742	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327996	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327997	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289466	0.82[EUR][1000 genomes]
rs13294931	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026031	0.97[AMR][1000 genomes];0.94[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];0.94[EUR][1000 genomes]
rs2943532	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs589362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs603947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs624075	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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];0.90[ASN][1000 genomes]
rs640297	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478977	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs649819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs657451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682682	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689696	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689697	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689744	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs689761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689804	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689860	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689911	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689986	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690063	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690528	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs690633	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694230	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700962	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7847983	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852346	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7871709	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816672	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816673	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816674	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816675	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816682	0.85[AMR][1000 genomes]
rs816683	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs816684	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs671058	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs671058	ERCC6L2	cis	Artery Tibial	GTEx
rs671058	C9orf102	cis	multi-tissue	Pritchard
rs671058	LOC286353	cis	multi-tissue	Pritchard
rs671058	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
4	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
6	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
7	chr9:98673600-98702200	Weak transcription	Small Intestine	intestine
8	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
9	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:98678000-98699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:98678000-98699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
13	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:98679400-98695200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:98679400-98698600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:98680800-98706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:98681800-98694400	Weak transcription	Fetal Stomach	stomach
18	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
19	chr9:98682400-98698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:98683200-98697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:98683400-98702600	Strong transcription	HSMM	muscle
22	chr9:98684200-98697200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:98684800-98695400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:98684800-98697800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:98685400-98699600	Strong transcription	Primary T cells from cord blood	blood
26	chr9:98685800-98698400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:98686000-98699200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:98686200-98699400	Weak transcription	NHEK	skin
29	chr9:98686400-98694600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:98686400-98695200	Weak transcription	K562	blood
31	chr9:98686400-98702200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
33	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:98686800-98696800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:98687200-98695800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:98687800-98694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:98687800-98694400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:98687800-98694400	Weak transcription	Fetal Intestine Large	intestine
40	chr9:98687800-98694400	Weak transcription	Fetal Intestine Small	intestine
41	chr9:98687800-98695400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:98687800-98695800	Weak transcription	Thymus	Thymus
43	chr9:98687800-98697600	Weak transcription	Ovary	ovary
44	chr9:98687800-98700600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr9:98687800-98701800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr9:98687800-98703400	Weak transcription	Hela-S3	cervix
47	chr9:98687800-98709000	Weak transcription	Lung	lung
48	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
49	chr9:98687800-98726000	Weak transcription	Gastric	stomach
50	chr9:98688000-98694800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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