Variant report

Variant	rs12569487
Chromosome Location	chr10:18847584-18847585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10430567	0.81[AFR][1000 genomes]
rs10764582	0.84[AFR][1000 genomes]
rs10764583	0.87[AFR][1000 genomes]
rs10764600	0.86[AFR][1000 genomes]
rs10764601	0.86[AFR][1000 genomes]
rs10764603	0.86[AFR][1000 genomes]
rs10828872	0.87[AFR][1000 genomes]
rs10828896	0.90[AFR][1000 genomes]
rs10828911	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10828965	0.86[AFR][1000 genomes]
rs10828975	0.86[AFR][1000 genomes]
rs11014892	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11015048	0.84[AFR][1000 genomes]
rs11525266	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12569474	0.90[AFR][1000 genomes]
rs12570792	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817494	0.88[AFR][1000 genomes]
rs4748488	0.87[AFR][1000 genomes]
rs4748492	0.87[AFR][1000 genomes]
rs57579336	0.87[AFR][1000 genomes]
rs62634837	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62634838	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62636218	0.87[AFR][1000 genomes]
rs6482533	0.83[AFR][1000 genomes]
rs7077722	0.83[AFR][1000 genomes]
rs7079325	0.88[AFR][1000 genomes]
rs72787951	0.88[AFR][1000 genomes]
rs72787963	0.86[AFR][1000 genomes]
rs7894016	0.86[AFR][1000 genomes]
rs7901598	0.90[AFR][1000 genomes]
rs7904263	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:95 , 50 per page) page: 1 2

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
17	esv18824	chr10:18841137-18862749	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
18	esv1815720	chr10:18841795-18853581	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
19	nsv550045	chr10:18841795-18854685	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
20	nsv550046	chr10:18841795-18855161	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
21	nsv550047	chr10:18841795-18855755	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
22	esv1847851	chr10:18841795-18857730	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
23	esv1850351	chr10:18841795-18857730	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
24	nsv550048	chr10:18841795-18857730	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
25	esv1808982	chr10:18841795-18858271	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
26	esv1817510	chr10:18841795-18858271	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
27	nsv550049	chr10:18841795-18858271	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
28	nsv550050	chr10:18841795-18858664	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
29	nsv550051	chr10:18841795-18859450	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
30	nsv550052	chr10:18841795-18860469	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
31	nsv550053	chr10:18841795-18861203	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
32	nsv550054	chr10:18841795-18862122	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
33	esv1802087	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
34	esv1805552	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
35	esv1807060	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
36	esv1812459	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
37	esv1834849	chr10:18841795-18862211	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
38	esv1836472	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
39	esv1842030	chr10:18841795-18862211	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
40	esv1850544	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
41	nsv550055	chr10:18841795-18862211	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
42	nsv550056	chr10:18841795-18862728	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
43	esv1845973	chr10:18841795-18872699	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
44	esv1793359	chr10:18841795-18872872	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
45	nsv550057	chr10:18843332-18858203	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
46	nsv550058	chr10:18843332-18859153	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
47	esv1843559	chr10:18843332-18859450	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
48	nsv550059	chr10:18843332-18859450	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
49	nsv550060	chr10:18843332-18860138	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
50	nsv550061	chr10:18843332-18860469	Strong transcription Weak transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12569487	RP11-499P20.2	cis	Whole Blood	GTEx
rs12569487	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs12569487	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs12569487	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs12569487	RP11-499P20.2	cis	Thyroid	GTEx
rs12569487	RP11-499P20.2	cis	lung	GTEx
rs12569487	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs12569487	NSUN6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:18824200-18850600	Weak transcription	NHLF	lung
3	chr10:18829200-18851200	Weak transcription	Esophagus	oesophagus
4	chr10:18830200-18851000	Weak transcription	Thymus	Thymus
5	chr10:18830400-18856600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr10:18831000-18850200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:18834400-18847800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:18838800-18849800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:18840600-18851200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
10	chr10:18840800-18851000	Weak transcription	Psoas Muscle	Psoas
11	chr10:18840800-18867200	Weak transcription	Fetal Thymus	thymus
12	chr10:18841400-18848800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
13	chr10:18841600-18849600	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr10:18841600-18849800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr10:18841600-18850000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr10:18841600-18850000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:18841600-18850000	ZNF genes & repeats	Fetal Lung	lung
18	chr10:18841600-18851400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
19	chr10:18841600-18851800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
20	chr10:18841600-18854600	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr10:18841600-18856200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr10:18841800-18849600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr10:18841800-18849800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:18841800-18850000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr10:18841800-18850000	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr10:18841800-18850000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr10:18841800-18853000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr10:18841800-18855400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:18842000-18847800	Weak transcription	Stomach Mucosa	stomach
30	chr10:18842000-18848600	Weak transcription	Placenta	Placenta
31	chr10:18842000-18849200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr10:18842000-18849200	ZNF genes & repeats	Fetal Brain Female	brain
33	chr10:18842000-18850000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:18842000-18851400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr10:18842000-18853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr10:18842000-18866800	Weak transcription	Left Ventricle	heart
37	chr10:18842000-18868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:18842000-18869200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:18842600-18849400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:18842600-18849800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr10:18842600-18850000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr10:18842800-18850000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:18842800-18850000	ZNF genes & repeats	Dnd41	blood
45	chr10:18843000-18849200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:18843000-18850000	ZNF genes & repeats	Adipose Nuclei	Adipose
47	chr10:18843200-18847800	ZNF genes & repeats	Fetal Muscle Leg	muscle
48	chr10:18843200-18852600	Strong transcription	Ovary	ovary
49	chr10:18843400-18849000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:18843400-18850000	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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