Variant report

Variant	rs6670208
Chromosome Location	chr1:10252667-10252668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1002076	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10492969	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10492971	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10492972	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10492973	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10864450	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10864453	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11121526	0.90[ASN][1000 genomes]
rs11121551	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11121552	0.87[CEU][hapmap]
rs11121555	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11121557	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11576866	0.84[CEU][hapmap]
rs11582123	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11585794	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11587309	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11587495	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12116966	0.96[ASN][1000 genomes]
rs12120042	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12120191	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12122107	0.86[EUR][1000 genomes]
rs12127604	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12130220	0.87[CEU][hapmap]
rs12130563	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12131441	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12133617	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12136376	0.87[CEU][hapmap]
rs12141246	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12141416	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12402052	0.91[CEU][hapmap]
rs12407992	0.87[CEU][hapmap]
rs12728071	0.84[ASN][1000 genomes]
rs12733312	0.84[CEU][hapmap]
rs12734551	0.87[CEU][hapmap]
rs12737239	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12740371	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12751375	0.88[CEU][hapmap]
rs12755094	0.88[CEU][hapmap]
rs12757288	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1339458	0.87[CEU][hapmap]
rs1467653	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1536262	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1536263	0.88[CEU][hapmap]
rs1538557	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1555849	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1556915	0.87[JPT][hapmap]
rs1556916	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1556917	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17034643	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17034821	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17396382	0.84[CEU][hapmap]
rs17400510	0.87[CEU][hapmap]
rs17401924	0.87[CEU][hapmap]
rs17401966	0.87[CEU][hapmap]
rs17410217	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17411502	0.87[CEU][hapmap]
rs1974293	0.84[ASN][1000 genomes]
rs2027330	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2039778	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2182326	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2185252	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2275424	0.83[CEU][hapmap]
rs35257796	0.94[ASN][1000 genomes]
rs3748575	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3748577	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3748578	0.87[CEU][hapmap]
rs3748581	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3753037	0.87[CEU][hapmap]
rs3828081	0.92[ASN][1000 genomes]
rs3903151	0.95[ASN][1000 genomes]
rs4240911	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4333852	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4348727	0.87[CEU][hapmap]
rs4475756	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4529713	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4623	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4845930	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4846197	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4846198	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4846199	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4846207	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4846208	0.87[CEU][hapmap]
rs4846209	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4846210	0.87[CEU][hapmap]
rs4846212	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4846216	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs61784566	0.86[EUR][1000 genomes]
rs61784570	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6541085	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6541089	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6660928	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661326	0.86[JPT][hapmap]
rs6670320	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696056	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6700866	0.87[CEU][hapmap]
rs7418410	0.81[JPT][hapmap]
rs746881	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7520935	0.87[CEU][hapmap]
rs7546364	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7546368	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7553228	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7553935	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8019	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs912962	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs912963	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9332414	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs946501	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs946503	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs946504	0.90[CHB][hapmap];0.95[JPT][hapmap]

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	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6670208	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
2	chr1:10236400-10258200	Weak transcription	HSMM	muscle
3	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:10241000-10254000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:10241000-10254200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:10241000-10254200	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:10241000-10254200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:10241000-10254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:10241000-10257200	Weak transcription	Ovary	ovary
11	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
12	chr1:10241200-10254000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:10241200-10254200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:10241200-10254200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:10241200-10259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:10241400-10253400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:10241400-10255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:10241600-10254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:10241600-10254000	Weak transcription	Osteobl	bone
20	chr1:10241800-10254000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:10244200-10256800	Weak transcription	Fetal Stomach	stomach
22	chr1:10247200-10254200	Weak transcription	Fetal Kidney	kidney
23	chr1:10247200-10255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:10248800-10253400	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:10250000-10261000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:10250000-10269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:10252200-10253600	Enhancers	HepG2	liver
28	chr1:10252400-10252800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:10252400-10252800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:10252400-10252800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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