Variant report

Variant	rs62559767
Chromosome Location	chr9:98777820-98777821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98769873..98772707-chr9:98776705..98779078,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10115110	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10117340	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10125109	0.81[EUR][1000 genomes]
rs10512245	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739622	0.86[EUR][1000 genomes]
rs10739705	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10760189	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10760261	0.87[EUR][1000 genomes]
rs10760262	0.87[EUR][1000 genomes]
rs10760269	0.86[EUR][1000 genomes]
rs10760679	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818574	0.83[EUR][1000 genomes]
rs10818746	0.86[EUR][1000 genomes]
rs10818899	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819650	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10819663	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10819668	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10819720	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10985156	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10985499	0.83[EUR][1000 genomes]
rs10985769	0.86[EUR][1000 genomes]
rs10987963	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10988755	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10988817	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10989035	0.83[AMR][1000 genomes]
rs1195130	0.86[AMR][1000 genomes]
rs11998982	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12000073	0.86[EUR][1000 genomes]
rs12340954	0.84[AMR][1000 genomes]
rs12343734	0.86[EUR][1000 genomes]
rs12345187	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12347675	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12348051	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12349742	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1327996	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1327997	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13299166	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1556026	0.80[EUR][1000 genomes]
rs2026031	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2296858	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2405371	0.83[EUR][1000 genomes]
rs2405372	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2943532	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs589362	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs596413	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs603947	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609296	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs617187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs623438	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs624075	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs625105	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62559026	0.83[EUR][1000 genomes]
rs640297	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6478977	0.82[EUR][1000 genomes]
rs649819	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657451	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666093	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667705	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs671058	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs682682	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs684455	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs686048	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs689619	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689696	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689697	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689710	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689738	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689744	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689761	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689804	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs689860	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689911	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689986	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690056	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690063	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690286	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690495	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690528	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690633	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs694230	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs700962	0.83[EUR][1000 genomes]
rs7847393	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7847983	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871709	0.82[EUR][1000 genomes]
rs816670	0.83[EUR][1000 genomes]
rs816672	0.83[EUR][1000 genomes]
rs816673	0.83[EUR][1000 genomes]
rs816674	0.83[EUR][1000 genomes]
rs816675	0.83[EUR][1000 genomes]
rs816678	0.82[EUR][1000 genomes]
rs816680	0.81[EUR][1000 genomes]
rs816683	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816684	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs966217	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62559767	ERCC6L2	cis	Artery Tibial	GTEx
rs62559767	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs62559767	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
2	chr9:98734600-98782400	Weak transcription	NHEK	skin
3	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
4	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
5	chr9:98741800-98778600	Weak transcription	NH-A	brain
6	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
7	chr9:98748000-98782600	Weak transcription	HMEC	breast
8	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:98759000-98780200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:98765800-98781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:98766400-98779800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:98766400-98780800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:98768600-98782600	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:98771200-98781200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:98771600-98778400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:98771600-98779200	Weak transcription	Fetal Brain Female	brain
18	chr9:98771600-98779600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:98771600-98779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:98771600-98781600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:98771600-98782600	Weak transcription	Placenta	Placenta
22	chr9:98771600-98782800	Weak transcription	A549	lung
23	chr9:98771600-98783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:98771800-98778800	Weak transcription	Osteobl	bone
25	chr9:98771800-98780800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:98771800-98781800	Weak transcription	Right Ventricle	heart
27	chr9:98771800-98782600	Weak transcription	Ovary	ovary
28	chr9:98772000-98779200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:98772000-98781400	Weak transcription	NHLF	lung
30	chr9:98772000-98781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:98772200-98778400	Weak transcription	HSMMtube	muscle
32	chr9:98772200-98779200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr9:98772200-98779200	Weak transcription	Spleen	Spleen
34	chr9:98772200-98780800	Weak transcription	Stomach Mucosa	stomach
35	chr9:98772200-98782600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:98772200-98782800	Weak transcription	Brain Angular Gyrus	brain
37	chr9:98772400-98778200	Weak transcription	K562	blood
38	chr9:98772400-98780600	Weak transcription	Fetal Heart	heart
39	chr9:98772600-98782400	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:98773000-98780400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:98773000-98781600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:98773000-98781600	Weak transcription	Brain Germinal Matrix	brain
43	chr9:98773600-98780800	Weak transcription	Small Intestine	intestine
44	chr9:98773600-98782600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:98773800-98779200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:98773800-98779200	Weak transcription	Aorta	Aorta
47	chr9:98773800-98779200	Weak transcription	Fetal Intestine Small	intestine
48	chr9:98773800-98779200	Weak transcription	Fetal Thymus	thymus
49	chr9:98773800-98779200	Weak transcription	Pancreas	Pancrea
50	chr9:98773800-98779400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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