Variant report

Variant	rs12219183
Chromosome Location	chr10:18929138-18929139
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18928489..18931214-chr10:18946847..18949825,2	MCF-7	breast:
2	chr10:18927647..18933802-chr10:18937639..18941916,7	K562	blood:
3	chr10:18921869..18924781-chr10:18927596..18930415,2	K562	blood:

Variant related genes	Relation type
ENSG00000165997	Chromatin interaction
ENSG00000152487	Chromatin interaction
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10430567	0.80[AFR][1000 genomes]
rs1055116	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10734063	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10741111	0.90[ASN][1000 genomes]
rs10741115	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10741129	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741132	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10764582	0.84[AMR][1000 genomes]
rs10764583	0.80[AMR][1000 genomes]
rs10764600	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764601	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764602	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10764603	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10764604	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10764605	0.87[ASN][1000 genomes]
rs10764625	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10764640	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10764691	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10828851	0.81[AMR][1000 genomes]
rs10828870	0.84[AMR][1000 genomes]
rs10828871	0.87[AMR][1000 genomes]
rs10828872	0.88[AMR][1000 genomes]
rs10828896	0.89[AMR][1000 genomes]
rs10828911	0.92[AMR][1000 genomes]
rs10828965	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10828975	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10828983	0.88[ASN][1000 genomes]
rs10828991	0.89[ASN][1000 genomes]
rs10829009	0.89[ASN][1000 genomes]
rs10829022	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10829037	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10829039	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10829040	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829058	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829060	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829070	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10829148	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10829151	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10829213	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11014892	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11015048	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11015077	0.88[ASN][1000 genomes]
rs11015196	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11015255	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11015312	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11015421	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11525266	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11593617	0.82[ASN][1000 genomes]
rs11812341	0.83[ASN][1000 genomes]
rs11815228	0.82[ASN][1000 genomes]
rs12359758	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569474	0.89[AMR][1000 genomes]
rs12762481	0.84[ASN][1000 genomes]
rs12766105	0.81[ASN][1000 genomes]
rs12780652	0.81[ASN][1000 genomes]
rs12785031	0.81[ASN][1000 genomes]
rs2272274	0.84[AMR][1000 genomes]
rs3740102	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740104	0.81[ASN][1000 genomes]
rs3817494	0.80[AMR][1000 genomes]
rs4445544	0.82[ASN][1000 genomes]
rs4747350	0.81[AMR][1000 genomes]
rs4748488	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4748492	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4748497	0.86[ASN][1000 genomes]
rs4748509	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5022622	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56410858	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57066269	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57579336	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62634837	0.83[AMR][1000 genomes]
rs62634838	0.83[AMR][1000 genomes]
rs62636218	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6482533	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6482597	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7077722	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7079325	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081461	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7081690	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081977	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085318	0.82[ASN][1000 genomes]
rs7087030	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7093454	0.82[ASN][1000 genomes]
rs7099260	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100880	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72787951	0.80[AMR][1000 genomes]
rs72787963	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7477076	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7894016	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7895784	0.88[ASN][1000 genomes]
rs7898781	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7899017	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7901598	0.92[AMR][1000 genomes]
rs7904263	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7907891	0.82[ASN][1000 genomes]
rs7909570	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7909845	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7910902	0.84[ASN][1000 genomes]
rs7917584	0.83[AMR][1000 genomes]
rs7919487	0.81[ASN][1000 genomes]
rs7923480	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv982911	chr10:18911989-18931479	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12219183	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs12219183	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs12219183	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs12219183	ARL5B	cis	Whole Blood	GTEx
rs12219183	ARL5B	cis	multi-tissue	Pritchard
rs12219183	RP11-499P20.2	cis	Thyroid	GTEx
rs12219183	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs12219183	NSUN6	cis	lung	GTEx
rs12219183	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs12219183	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12219183	RP11-499P20.2	cis	lung	GTEx
rs12219183	RP11-499P20.2	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916800-18930400	Weak transcription	Dnd41	blood
3	chr10:18916800-18935200	Weak transcription	K562	blood
4	chr10:18916800-18936200	Weak transcription	A549	lung
5	chr10:18916800-18937000	Weak transcription	GM12878-XiMat	blood
6	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
7	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
8	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
9	chr10:18917000-18929200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:18917000-18930200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:18917000-18930200	Weak transcription	Fetal Stomach	stomach
12	chr10:18917000-18930400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:18917000-18930400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr10:18917000-18930400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:18917000-18930400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:18917000-18930400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:18917000-18930400	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:18917000-18930600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:18917000-18930600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr10:18917000-18930600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:18917000-18930600	Weak transcription	Left Ventricle	heart
22	chr10:18917000-18930800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:18917000-18932400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:18917000-18932600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:18917000-18934200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:18917000-18934200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:18917000-18934400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:18917000-18934600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:18917000-18934600	Weak transcription	Fetal Brain Female	brain
30	chr10:18917000-18934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:18917000-18934800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:18917000-18935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:18917000-18935000	Weak transcription	Primary T cells from cord blood	blood
34	chr10:18917000-18936800	Weak transcription	Brain Germinal Matrix	brain
35	chr10:18917000-18937200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr10:18917000-18937400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:18917000-18938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:18917000-18938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:18917000-18938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:18917000-18938200	Weak transcription	Brain Angular Gyrus	brain
44	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr10:18917000-18938400	Weak transcription	Ovary	ovary
46	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:18917000-18938800	Weak transcription	HSMM	muscle
49	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
50	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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