Variant report

Variant	rs12359758
Chromosome Location	chr10:18935116-18935117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18929497..18932239-chr10:18933812..18935882,2	MCF-7	breast:
2	chr10:18933676..18935370-chr10:18939800..18942129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10400076	0.81[AMR][1000 genomes]
rs1055116	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10734063	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10741111	0.88[ASN][1000 genomes]
rs10741115	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10741129	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741132	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10764582	0.87[AMR][1000 genomes]
rs10764583	0.83[AMR][1000 genomes]
rs10764600	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10764601	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10764602	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10764603	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10764604	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10764605	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10764625	0.89[ASN][1000 genomes]
rs10764640	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10764691	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10828851	0.84[AMR][1000 genomes]
rs10828870	0.87[AMR][1000 genomes]
rs10828871	0.90[AMR][1000 genomes]
rs10828872	0.91[AMR][1000 genomes]
rs10828896	0.92[AMR][1000 genomes]
rs10828911	0.95[AMR][1000 genomes]
rs10828965	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10828975	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10828983	0.87[ASN][1000 genomes]
rs10828991	0.89[ASN][1000 genomes]
rs10829009	0.89[ASN][1000 genomes]
rs10829022	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829037	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10829039	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10829040	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10829058	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10829060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10829070	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829148	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10829151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10829213	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11014892	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11015048	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11015077	0.87[ASN][1000 genomes]
rs11015196	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015255	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11015312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11525266	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11540309	0.81[ASN][1000 genomes]
rs11593617	0.81[ASN][1000 genomes]
rs11812341	0.83[ASN][1000 genomes]
rs11815228	0.81[ASN][1000 genomes]
rs12219183	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569474	0.92[AMR][1000 genomes]
rs12762481	0.82[ASN][1000 genomes]
rs12780652	0.83[ASN][1000 genomes]
rs12785031	0.81[ASN][1000 genomes]
rs2272274	0.87[AMR][1000 genomes]
rs3740102	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740104	0.82[ASN][1000 genomes]
rs3817494	0.83[AMR][1000 genomes]
rs4445544	0.81[ASN][1000 genomes]
rs4747350	0.83[AMR][1000 genomes]
rs4748488	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4748492	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4748497	0.84[ASN][1000 genomes]
rs4748509	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5022622	0.89[ASN][1000 genomes]
rs56410858	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57066269	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57579336	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62634837	0.86[AMR][1000 genomes]
rs62634838	0.86[AMR][1000 genomes]
rs62636218	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6482533	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6482597	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7077722	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7079325	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7081461	0.87[ASN][1000 genomes]
rs7081690	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7081977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085318	0.81[ASN][1000 genomes]
rs7087030	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7093454	0.81[ASN][1000 genomes]
rs7099260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7100880	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72787951	0.83[AMR][1000 genomes]
rs72787963	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7477076	0.88[ASN][1000 genomes]
rs7894016	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7895784	0.87[ASN][1000 genomes]
rs7898781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7899017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7901598	0.95[AMR][1000 genomes]
rs7904263	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7907891	0.81[ASN][1000 genomes]
rs7909570	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7909845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7910902	0.86[ASN][1000 genomes]
rs7917584	0.86[AMR][1000 genomes]
rs7922550	0.82[AMR][1000 genomes]
rs7922829	0.82[AMR][1000 genomes]
rs7923480	0.84[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	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	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12359758	RP11-499P20.2	cis	Thyroid	GTEx
rs12359758	ARL5B	cis	multi-tissue	Pritchard
rs12359758	ARL5B	cis	Whole Blood	GTEx
rs12359758	RP11-499P20.2	cis	lung	GTEx
rs12359758	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs12359758	RP11-499P20.2	cis	Whole Blood	GTEx
rs12359758	NSUN6	cis	lung	GTEx
rs12359758	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs12359758	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12359758	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs12359758	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs12359758	CACNB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18905000-18938200	Weak transcription	Hela-S3	cervix
2	chr10:18916800-18935200	Weak transcription	K562	blood
3	chr10:18916800-18936200	Weak transcription	A549	lung
4	chr10:18916800-18937000	Weak transcription	GM12878-XiMat	blood
5	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
6	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
7	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
8	chr10:18917000-18936800	Weak transcription	Brain Germinal Matrix	brain
9	chr10:18917000-18937200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:18917000-18937400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr10:18917000-18938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:18917000-18938200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr10:18917000-18938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:18917000-18938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:18917000-18938200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:18917000-18938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:18917000-18938200	Weak transcription	Brain Angular Gyrus	brain
18	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:18917000-18938400	Weak transcription	Ovary	ovary
20	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:18917000-18938800	Weak transcription	HSMM	muscle
23	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
24	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:18917000-18940200	Weak transcription	Lung	lung
27	chr10:18917200-18935600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:18917200-18937800	Weak transcription	Adipose Nuclei	Adipose
29	chr10:18921400-18939000	Weak transcription	Right Ventricle	heart
30	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:18923200-18936600	Weak transcription	Fetal Brain Male	brain
32	chr10:18924800-18937800	Weak transcription	Fetal Lung	lung
33	chr10:18925200-18937600	Weak transcription	Fetal Heart	heart
34	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
36	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
37	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
38	chr10:18926400-18938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:18926600-18938200	Weak transcription	NHEK	skin
40	chr10:18927400-18939600	Weak transcription	Pancreas	Pancrea
41	chr10:18927800-18937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:18928000-18938400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:18928200-18938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:18928200-18939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:18928400-18938800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr10:18928800-18936000	Weak transcription	NH-A	brain
47	chr10:18928800-18937800	Weak transcription	Brain Anterior Caudate	brain
48	chr10:18928800-18939600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr10:18928800-18939600	Weak transcription	Gastric	stomach
50	chr10:18929000-18937000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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