Variant report

Variant	rs7901598
Chromosome Location	chr10:18839779-18839780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10400076	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10430567	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1055116	0.91[AMR][1000 genomes]
rs10734063	0.95[AMR][1000 genomes]
rs10741091	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10741115	0.97[AMR][1000 genomes]
rs10741129	0.89[AMR][1000 genomes]
rs10741132	0.88[AMR][1000 genomes]
rs10764582	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10764583	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10764600	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10764601	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764602	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10764603	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764604	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10764605	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10764640	0.92[AMR][1000 genomes]
rs10764691	0.87[AMR][1000 genomes]
rs10828851	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10828870	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10828871	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10828872	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828896	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828911	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10828965	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10828967	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10828975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829022	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10829037	0.96[AMR][1000 genomes]
rs10829039	0.97[AMR][1000 genomes]
rs10829040	0.88[AMR][1000 genomes]
rs10829058	0.93[AMR][1000 genomes]
rs10829060	0.95[AMR][1000 genomes]
rs10829070	0.93[AMR][1000 genomes]
rs10829151	0.95[AMR][1000 genomes]
rs10829213	0.87[AMR][1000 genomes]
rs11014892	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11015048	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015196	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11015255	0.89[AMR][1000 genomes]
rs11015312	0.95[AMR][1000 genomes]
rs11015421	0.95[AMR][1000 genomes]
rs11525266	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12219183	0.92[AMR][1000 genomes]
rs12359758	0.95[AMR][1000 genomes]
rs12569474	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12569487	0.90[AFR][1000 genomes]
rs12570792	0.82[AFR][1000 genomes]
rs2272274	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3740102	0.93[AMR][1000 genomes]
rs3817494	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4747349	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4747350	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4748488	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748492	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748509	0.86[AMR][1000 genomes]
rs56410858	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs57066269	0.93[AMR][1000 genomes]
rs57579336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62634837	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62634838	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62636218	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6482533	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6482597	0.91[AMR][1000 genomes]
rs7077722	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7079325	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7081690	0.92[AMR][1000 genomes]
rs7081977	0.95[AMR][1000 genomes]
rs7087030	0.91[AMR][1000 genomes]
rs7088091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7099260	0.95[AMR][1000 genomes]
rs7100880	0.84[AMR][1000 genomes]
rs72787951	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72787963	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7894016	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7895784	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7898781	0.95[AMR][1000 genomes]
rs7899017	0.95[AMR][1000 genomes]
rs7904263	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7909570	0.87[AMR][1000 genomes]
rs7909845	0.88[AMR][1000 genomes]
rs7917584	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7922550	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7922829	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1835982	chr10:18833550-18872699	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv511455	chr10:18837285-18854168	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
13	nsv550043	chr10:18837285-18859153	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
14	esv1814421	chr10:18839350-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
15	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7901598	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs7901598	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs7901598	ARL5B	cis	Whole Blood	GTEx
rs7901598	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs7901598	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs7901598	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7901598	RP11-499P20.2	cis	Whole Blood	GTEx
rs7901598	RP11-499P20.2	cis	lung	GTEx
rs7901598	RP11-499P20.2	cis	Thyroid	GTEx
rs7901598	NSUN6	cis	lung	GTEx
rs7901598	NSUN6	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18815200-18843600	Weak transcription	A549	lung
2	chr10:18816400-18841800	Strong transcription	Liver	Liver
3	chr10:18820800-18841600	Weak transcription	Hela-S3	cervix
4	chr10:18822000-18840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:18822800-18841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:18824200-18846200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:18824200-18850600	Weak transcription	NHLF	lung
9	chr10:18825600-18841800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:18827200-18842000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:18827200-18845200	Weak transcription	NHEK	skin
12	chr10:18827400-18841600	Weak transcription	HMEC	breast
13	chr10:18828600-18841600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr10:18828600-18841600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr10:18828600-18841800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:18828600-18841800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:18828600-18841800	Weak transcription	Pancreas	Pancrea
18	chr10:18828600-18843000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:18828600-18843400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:18828600-18844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:18828600-18845400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:18828800-18846000	Weak transcription	Spleen	Spleen
23	chr10:18829000-18840400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:18829000-18841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:18829200-18851200	Weak transcription	Esophagus	oesophagus
26	chr10:18829800-18844000	Weak transcription	Brain Angular Gyrus	brain
27	chr10:18830000-18842000	Weak transcription	Fetal Brain Female	brain
28	chr10:18830000-18842400	Weak transcription	Brain Germinal Matrix	brain
29	chr10:18830200-18841400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:18830200-18841800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:18830200-18841800	Weak transcription	Aorta	Aorta
32	chr10:18830200-18851000	Weak transcription	Thymus	Thymus
33	chr10:18830400-18840000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:18830400-18840200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:18830400-18840400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:18830400-18840400	Weak transcription	Brain Anterior Caudate	brain
37	chr10:18830400-18840400	Weak transcription	HSMMtube	muscle
38	chr10:18830400-18841600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr10:18830400-18841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr10:18830400-18841800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:18830400-18841800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr10:18830400-18841800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr10:18830400-18841800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr10:18830400-18841800	Weak transcription	Brain Substantia Nigra	brain
45	chr10:18830400-18841800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:18830400-18843000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr10:18830400-18856600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:18830600-18840200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:18830600-18840200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr10:18830600-18840200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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