Variant report

Variant	rs12403443
Chromosome Location	chr1:10423988-10423989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1002076	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs10492969	0.83[CHD][hapmap]
rs10492972	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs1049887	0.83[EUR][1000 genomes]
rs11121533	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11121544	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11121551	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs11121552	1.00[ASW][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11121557	0.83[CHD][hapmap]
rs11576654	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11576866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11578694	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11578788	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11579365	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs11585760	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11587309	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs12119477	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120042	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs12120191	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs12127553	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12129035	0.83[AMR][1000 genomes]
rs12130220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12131441	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs12132635	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136376	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12137456	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141416	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs12402052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12406776	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12407992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12408019	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12409754	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs12733312	0.80[JPT][hapmap]
rs12734068	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12734551	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12751375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs12755094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1339458	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1467653	0.83[CHD][hapmap]
rs1536262	0.83[CHD][hapmap]
rs1536263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538557	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs1555849	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs1556916	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs1556917	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs17034643	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs17034821	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs17400510	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17401924	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17401966	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17410217	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs17410793	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17411502	0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1889309	0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap]
rs2004034	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039778	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs2182326	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs2185252	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs2275424	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34215045	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34225619	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35766535	0.84[AMR][1000 genomes]
rs35837142	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3737155	0.83[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs3748577	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs3748578	0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748581	0.83[CHD][hapmap]
rs3753037	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4240911	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs4259656	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4333852	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs4348727	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4475756	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs4529713	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs4845933	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4846197	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs4846208	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4846209	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs4846210	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4846212	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs4846216	0.83[CHD][hapmap]
rs4846219	0.83[CHD][hapmap]
rs4846221	0.83[CHD][hapmap]
rs58053556	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58549151	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58697740	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60743860	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541085	0.83[CHD][hapmap]
rs6674843	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6682868	0.83[CHD][hapmap]
rs6700866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs746881	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs7520651	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7520935	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7530167	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7546368	0.83[CHD][hapmap]
rs7553935	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs8019	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs912962	0.83[CHD][hapmap]
rs912963	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs9332414	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs946501	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs946503	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs946504	0.83[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12403443	KIF1B	cis	Thyroid	GTEx
rs12403443	UTS2	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:10394200-10441800	Strong transcription	Liver	Liver
11	chr1:10395600-10425200	Weak transcription	Thymus	Thymus
12	chr1:10397800-10425400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:10397800-10434800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:10398000-10438000	Weak transcription	GM12878-XiMat	blood
15	chr1:10398400-10425400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10400200-10438200	Weak transcription	Stomach Mucosa	stomach
17	chr1:10400600-10434600	Weak transcription	K562	blood
18	chr1:10400600-10446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10400600-10447400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:10402600-10437200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:10404400-10433800	Weak transcription	Dnd41	blood
22	chr1:10409000-10425200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:10409000-10427800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:10409200-10425200	Weak transcription	Fetal Thymus	thymus
25	chr1:10409400-10425200	Weak transcription	Psoas Muscle	Psoas
26	chr1:10409800-10447400	Weak transcription	Small Intestine	intestine
27	chr1:10411600-10431200	Weak transcription	HUVEC	blood vessel
28	chr1:10412800-10425200	Weak transcription	Right Ventricle	heart
29	chr1:10413600-10425200	Weak transcription	Colonic Mucosa	Colon
30	chr1:10416600-10424200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:10418400-10424200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:10418400-10445600	Strong transcription	Fetal Brain Female	brain
33	chr1:10418600-10427000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:10419200-10424200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:10419200-10426600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr1:10419200-10437800	Weak transcription	Right Atrium	heart
37	chr1:10419200-10442800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:10419800-10441200	Strong transcription	Fetal Stomach	stomach
39	chr1:10420000-10440000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:10420200-10424000	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:10420200-10424200	Strong transcription	Adipose Nuclei	Adipose
42	chr1:10420200-10424200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr1:10420200-10426600	Strong transcription	HSMMtube	muscle
44	chr1:10420200-10426800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:10420200-10427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:10420200-10429600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:10420200-10432800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:10420200-10445000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:10420200-10446000	Strong transcription	Brain Germinal Matrix	brain
50	chr1:10420800-10424000	Strong transcription	HSMM	muscle

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