Variant report

Variant	rs12119477
Chromosome Location	chr1:10410916-10410917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1002076	0.83[EUR][1000 genomes]
rs10492972	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10492973	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1049887	0.92[EUR][1000 genomes]
rs1065828	0.83[AMR][1000 genomes]
rs11121531	0.82[EUR][1000 genomes]
rs11121532	0.85[EUR][1000 genomes]
rs11121533	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11121537	0.83[AMR][1000 genomes]
rs11121539	0.84[AMR][1000 genomes]
rs11121544	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11121545	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11121552	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11121560	0.83[EUR][1000 genomes]
rs11576654	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11576866	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578694	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11578788	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580789	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11585760	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585794	0.81[EUR][1000 genomes]
rs11587309	0.83[EUR][1000 genomes]
rs11587495	0.82[EUR][1000 genomes]
rs11587854	0.83[EUR][1000 genomes]
rs12120042	0.82[AMR][1000 genomes]
rs12120191	0.82[AMR][1000 genomes]
rs12127553	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12127604	0.82[AMR][1000 genomes]
rs12129035	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12130220	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130563	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12131441	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12132134	0.83[AMR][1000 genomes]
rs12132635	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136376	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12137456	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12137880	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12139981	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12141201	0.83[EUR][1000 genomes]
rs12141416	0.84[EUR][1000 genomes]
rs12402052	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12403443	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403465	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12406776	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12407992	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12408019	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12409754	0.83[EUR][1000 genomes]
rs12409933	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12722830	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12725210	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12734068	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12734551	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12738317	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12753426	0.83[AMR][1000 genomes]
rs12755094	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12755363	0.86[EUR][1000 genomes]
rs12759696	0.82[EUR][1000 genomes]
rs1339458	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1536263	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555849	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1556916	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1556917	0.82[AMR][1000 genomes]
rs17034821	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17400510	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17401924	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17401966	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17410217	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17410793	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17411502	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1889309	0.87[EUR][1000 genomes]
rs2004034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2039778	0.82[AMR][1000 genomes]
rs2148152	0.81[AMR][1000 genomes]
rs2182326	0.84[AMR][1000 genomes]
rs2185252	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2275424	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276100	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34215045	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34225619	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34636442	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35388505	0.86[EUR][1000 genomes]
rs35766535	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35837142	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3737155	0.83[EUR][1000 genomes]
rs3748577	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3748578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748579	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3753037	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4240911	0.82[EUR][1000 genomes]
rs4259656	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4333852	0.84[AMR][1000 genomes]
rs4475756	0.84[AMR][1000 genomes]
rs4623	0.82[AMR][1000 genomes]
rs4845932	0.81[AMR][1000 genomes]
rs4845933	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845934	0.88[EUR][1000 genomes]
rs4846205	0.82[EUR][1000 genomes]
rs4846208	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4846210	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4846212	0.83[AMR][1000 genomes]
rs4846213	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58053556	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58549151	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58697740	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60743860	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61326491	0.80[AMR][1000 genomes]
rs61778376	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61778399	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61778401	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61778402	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61778403	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61778404	0.82[EUR][1000 genomes]
rs6541089	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6674843	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6700866	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs746881	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7520651	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7520935	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7524693	0.81[AMR][1000 genomes]
rs7530167	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7546364	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7553228	0.82[AMR][1000 genomes]
rs7553935	0.82[AMR][1000 genomes]
rs912961	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12119477	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
8	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:10394200-10411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:10394200-10413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:10394200-10414200	Strong transcription	Brain Germinal Matrix	brain
15	chr1:10394200-10414200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr1:10394200-10415800	Strong transcription	Adipose Nuclei	Adipose
17	chr1:10394200-10415800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:10394200-10441800	Strong transcription	Liver	Liver
19	chr1:10394400-10411200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:10394400-10411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:10394400-10413400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:10394400-10414200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:10395600-10425200	Weak transcription	Thymus	Thymus
24	chr1:10397600-10421000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:10397800-10425400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:10397800-10434800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:10398000-10421000	Weak transcription	NHEK	skin
28	chr1:10398000-10438000	Weak transcription	GM12878-XiMat	blood
29	chr1:10398400-10425400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:10399000-10420800	Weak transcription	NHLF	lung
31	chr1:10400000-10416200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:10400200-10413600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:10400200-10438200	Weak transcription	Stomach Mucosa	stomach
34	chr1:10400600-10434600	Weak transcription	K562	blood
35	chr1:10400600-10446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:10400600-10447400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:10400800-10414000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:10401600-10412600	Strong transcription	Brain Angular Gyrus	brain
39	chr1:10401600-10420800	Weak transcription	Fetal Heart	heart
40	chr1:10401600-10421000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:10401800-10415200	Strong transcription	HSMMtube	muscle
42	chr1:10402200-10418400	Weak transcription	A549	lung
43	chr1:10402600-10437200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:10403000-10413600	Strong transcription	Fetal Stomach	stomach
45	chr1:10403800-10421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:10404200-10421000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:10404400-10421000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:10404400-10421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:10404400-10433800	Weak transcription	Dnd41	blood
50	chr1:10404600-10421400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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