Variant report

Variant	rs667705
Chromosome Location	chr9:98746414-98746415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98745793..98747738-chr9:98750041..98751835,2	K562	blood:
2	chr9:98746100..98748264-chr9:98759830..98761515,2	MCF-7	breast:
3	chr9:98746263..98748269-chr9:98754898..98757748,2	K562	blood:
4	chr9:98636021..98638369-chr9:98744336..98747127,2	K562	blood:
5	chr9:98719153..98720916-chr9:98745927..98748838,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10115110	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10117340	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10125109	0.83[EUR][1000 genomes]
rs10512245	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739622	0.88[EUR][1000 genomes]
rs10739705	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760189	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10760261	0.88[EUR][1000 genomes]
rs10760262	0.88[EUR][1000 genomes]
rs10760269	0.88[EUR][1000 genomes]
rs10760679	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10818574	0.84[EUR][1000 genomes]
rs10818746	0.88[EUR][1000 genomes]
rs10818899	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10819650	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819663	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10819668	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10819720	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10985156	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10985499	0.84[EUR][1000 genomes]
rs10985769	0.88[EUR][1000 genomes]
rs10987963	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988755	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988817	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10989035	0.81[AMR][1000 genomes]
rs1195130	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11998982	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12000073	0.88[EUR][1000 genomes]
rs12340954	0.82[AMR][1000 genomes]
rs12343734	0.88[EUR][1000 genomes]
rs12345187	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12347675	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12348051	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12349742	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1327996	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1327997	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13294931	0.81[EUR][1000 genomes]
rs13299166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2026031	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296858	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2405134	0.82[EUR][1000 genomes]
rs2405371	0.85[EUR][1000 genomes]
rs2405372	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2943532	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs589362	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs596413	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603947	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609296	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs617187	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs623438	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs624075	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625105	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62559026	0.85[EUR][1000 genomes]
rs62559767	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs640297	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6478977	0.83[EUR][1000 genomes]
rs649819	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs657451	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666093	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs671058	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682682	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs684455	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs686048	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs689619	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689696	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689697	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689710	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689738	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689744	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689761	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689804	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689860	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689911	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689986	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690056	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690063	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690286	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690495	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690528	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs690633	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694230	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs700962	0.85[EUR][1000 genomes]
rs7847393	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7847983	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7852346	0.80[EUR][1000 genomes]
rs7871709	0.83[EUR][1000 genomes]
rs816670	0.85[EUR][1000 genomes]
rs816672	0.85[EUR][1000 genomes]
rs816673	0.85[EUR][1000 genomes]
rs816674	0.85[EUR][1000 genomes]
rs816675	0.85[EUR][1000 genomes]
rs816678	0.84[EUR][1000 genomes]
rs816680	0.83[EUR][1000 genomes]
rs816683	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816684	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs966217	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs667705	ERCC6L2	cis	Artery Tibial	GTEx
rs667705	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs667705	C9orf102	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
4	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
5	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
7	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
8	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
10	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:98722400-98747800	Weak transcription	Fetal Heart	heart
13	chr9:98723800-98749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:98726400-98767800	Weak transcription	Gastric	stomach
15	chr9:98730600-98751200	Weak transcription	Small Intestine	intestine
16	chr9:98732200-98747400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:98732200-98751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:98733000-98749600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:98734600-98749800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr9:98734600-98764400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:98734600-98782400	Weak transcription	NHEK	skin
23	chr9:98735200-98751600	Weak transcription	NHDF-Ad	bronchial
24	chr9:98735400-98747200	Weak transcription	A549	lung
25	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
26	chr9:98735800-98747200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:98735800-98747200	Weak transcription	HMEC	breast
28	chr9:98735800-98748400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:98735800-98764200	Weak transcription	Placenta	Placenta
30	chr9:98735800-98766600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:98735800-98770600	Weak transcription	K562	blood
32	chr9:98735800-98771200	Weak transcription	HepG2	liver
33	chr9:98736000-98746800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:98736000-98747200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr9:98736000-98747400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:98736000-98747600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:98736000-98749800	Weak transcription	Lung	lung
38	chr9:98736000-98751400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:98736200-98752800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr9:98736400-98747400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:98736400-98747600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:98736400-98749200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:98736400-98751000	Weak transcription	Ovary	ovary
44	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
45	chr9:98736800-98747200	Weak transcription	Primary B cells from cord blood	blood
46	chr9:98737000-98766800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:98738800-98756400	Weak transcription	Aorta	Aorta
48	chr9:98740800-98747200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:98741600-98747200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:98741600-98747800	Weak transcription	Primary B cells from peripheral blood	blood

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