Variant report

Variant	rs1195130
Chromosome Location	chr9:98641472-98641473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98640806..98643055-chr9:98646394..98647992,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10115110	0.94[AMR][1000 genomes]
rs10117340	0.94[AMR][1000 genomes]
rs10125109	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10512242	0.85[AMR][1000 genomes]
rs10512245	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10739622	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739705	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10760189	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10760261	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10760262	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10760269	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10760679	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10818574	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10818746	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10818899	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819650	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10819663	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10819668	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10819720	0.86[AMR][1000 genomes]
rs10985156	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10985499	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10985769	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10987963	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10988755	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10988817	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10989035	0.88[AMR][1000 genomes]
rs11998982	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12000073	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12340954	0.87[AMR][1000 genomes]
rs12343734	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12345187	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12347675	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348051	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12349742	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1327996	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1327997	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13289466	0.83[ASN][1000 genomes]
rs13294931	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13298093	0.85[AMR][1000 genomes]
rs13299166	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2026031	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296858	0.94[AMR][1000 genomes]
rs2405134	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2405371	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2405372	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2943532	0.92[AMR][1000 genomes]
rs589362	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs596413	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603947	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs609296	0.86[AMR][1000 genomes]
rs617187	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs623438	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs624075	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs625105	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62559026	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62559767	0.86[AMR][1000 genomes]
rs640297	0.90[AMR][1000 genomes]
rs6478977	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs649819	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs657451	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs666093	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs667705	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs671058	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs682682	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs684455	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs686048	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689619	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689696	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689697	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689710	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689738	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689744	0.94[AMR][1000 genomes]
rs689761	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689804	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689860	0.87[AMR][1000 genomes]
rs689911	0.88[AMR][1000 genomes]
rs689986	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690056	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690063	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs690286	0.94[AMR][1000 genomes]
rs690495	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690528	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs690633	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694230	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs700962	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7847393	0.92[AMR][1000 genomes]
rs7847983	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7852346	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7871709	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs816670	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816672	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816673	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816674	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816675	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816678	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs816680	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs816682	0.88[AMR][1000 genomes]
rs816683	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816684	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs966217	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1195130	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs1195130	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs1195130	LINC00476	cis	Artery Aorta	GTEx
rs1195130	ERCC6L2	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:98638800-98648400	Weak transcription	Lung	lung
3	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
5	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
6	chr9:98639200-98644200	Weak transcription	Aorta	Aorta
7	chr9:98639400-98641600	Weak transcription	Fetal Kidney	kidney
8	chr9:98639400-98641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:98639400-98643200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:98639400-98643400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:98639400-98644000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:98639400-98647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
16	chr9:98639400-98678000	Weak transcription	Ovary	ovary
17	chr9:98639600-98641800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:98639600-98644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:98639600-98646200	Weak transcription	HSMMtube	muscle
20	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:98639800-98641800	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:98639800-98643200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:98639800-98643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:98639800-98643200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr9:98639800-98644000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:98640000-98641600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr9:98640000-98641600	Weak transcription	Osteobl	bone
31	chr9:98640000-98641800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:98640000-98641800	Weak transcription	Fetal Heart	heart
33	chr9:98640000-98641800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:98640000-98641800	Weak transcription	Hela-S3	cervix
35	chr9:98640000-98642000	Weak transcription	NHDF-Ad	bronchial
36	chr9:98640000-98642600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:98640000-98643200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:98640000-98643400	Weak transcription	Primary B cells from cord blood	blood
39	chr9:98640000-98643400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:98640000-98643600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:98640000-98643600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:98640000-98643600	Weak transcription	Adipose Nuclei	Adipose
43	chr9:98640000-98643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:98640000-98643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:98640000-98643800	Weak transcription	Brain Germinal Matrix	brain
46	chr9:98640000-98644200	Weak transcription	Fetal Muscle Leg	muscle
47	chr9:98640000-98644200	Weak transcription	Gastric	stomach
48	chr9:98640000-98644200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:98640000-98644400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:98640000-98645400	Weak transcription	Stomach Smooth Muscle	stomach

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