Variant report

Variant	rs10988817
Chromosome Location	chr9:98722646-98722647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10115110	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10117340	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10125109	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10512242	0.81[AMR][1000 genomes]
rs10512245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10739705	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760189	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760261	0.95[CEU][hapmap];0.96[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760269	0.95[CEU][hapmap];0.96[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818574	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10818899	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819650	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10819663	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985156	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10985499	0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10987963	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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];0.89[EUR][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12345187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[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];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12349742	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1327996	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1327997	0.84[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	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026031	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296858	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2405134	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2405371	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2405372	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2943532	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs589362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs603947	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624075	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62559026	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62559767	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640297	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478977	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs649819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs671058	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]
rs682682	0.86[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689696	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689697	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689744	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689804	1.00[CEU][hapmap];0.81[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];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689986	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs690056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690063	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690528	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690633	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs694230	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs700962	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7852346	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7871709	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816670	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816672	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816673	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816674	0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816675	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816682	0.85[AMR][1000 genomes]
rs816683	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs816684	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.98[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10988817	ERCC6L2	cis	Artery Tibial	GTEx
rs10988817	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10988817	LOC286353	cis	multi-tissue	Pritchard
rs10988817		cis	Lymphoblastoid	GTEx
rs10988817	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs10988817	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	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
2	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:98687800-98726000	Weak transcription	Gastric	stomach
4	chr9:98695800-98742400	Weak transcription	NHLF	lung
5	chr9:98705400-98734200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
7	chr9:98706800-98734000	Weak transcription	Hela-S3	cervix
8	chr9:98709800-98727800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:98710000-98734200	Weak transcription	HMEC	breast
10	chr9:98710000-98735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
12	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
14	chr9:98716600-98734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:98718600-98729600	Weak transcription	NHDF-Ad	bronchial
16	chr9:98718800-98729400	Weak transcription	HepG2	liver
17	chr9:98719000-98733800	Weak transcription	NHEK	skin
18	chr9:98719000-98738600	Weak transcription	Aorta	Aorta
19	chr9:98719000-98743800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
21	chr9:98719200-98722800	Weak transcription	Fetal Brain Male	brain
22	chr9:98719200-98723000	Weak transcription	HSMMtube	muscle
23	chr9:98719200-98725000	Weak transcription	Fetal Stomach	stomach
24	chr9:98719200-98726000	Weak transcription	Primary B cells from cord blood	blood
25	chr9:98719200-98726000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:98719200-98728800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:98719200-98729200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:98719200-98733600	Weak transcription	Fetal Intestine Large	intestine
29	chr9:98719200-98734200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:98719200-98734200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:98719200-98734200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:98719200-98734200	Weak transcription	Esophagus	oesophagus
33	chr9:98719200-98734200	Weak transcription	Lung	lung
34	chr9:98719200-98734200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:98719200-98734200	Weak transcription	Thymus	Thymus
36	chr9:98719200-98734200	Weak transcription	K562	blood
37	chr9:98719200-98734800	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:98719200-98744000	Weak transcription	Brain Substantia Nigra	brain
39	chr9:98719200-98744400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
41	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
43	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
44	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:98719400-98723400	Weak transcription	NH-A	brain
46	chr9:98719400-98724800	Weak transcription	Fetal Lung	lung
47	chr9:98719400-98725800	Weak transcription	Left Ventricle	heart
48	chr9:98719400-98726000	Weak transcription	Ovary	ovary
49	chr9:98719400-98728600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:98719400-98728600	Weak transcription	Adipose Nuclei	Adipose

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