Variant report

Variant	rs12122107
Chromosome Location	chr1:10251449-10251450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1002076	0.87[CEU][hapmap]
rs10492971	0.81[CEU][hapmap]
rs10492972	0.91[CEU][hapmap]
rs10492973	0.81[CEU][hapmap]
rs11121528	0.83[ASN][1000 genomes]
rs11121551	0.80[CEU][hapmap]
rs11121552	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11576866	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs11582123	0.92[CEU][hapmap]
rs11585794	0.88[CEU][hapmap]
rs11587309	0.91[CEU][hapmap]
rs11587495	0.92[CEU][hapmap]
rs12117765	0.83[ASN][1000 genomes]
rs12120042	0.80[CEU][hapmap]
rs12120191	0.80[CEU][hapmap]
rs12127604	0.82[CEU][hapmap]
rs12130220	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12130563	0.92[CEU][hapmap]
rs12131441	0.91[CEU][hapmap]
rs12136376	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12141246	0.81[CEU][hapmap]
rs12141416	0.91[CEU][hapmap]
rs12402052	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs12403443	0.89[JPT][hapmap]
rs12407992	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12733312	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs12734551	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12737239	0.92[CEU][hapmap]
rs12751375	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12755094	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs12757288	0.81[CEU][hapmap]
rs12757820	0.83[ASN][1000 genomes]
rs1339458	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1396	0.88[EUR][1000 genomes]
rs1536263	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs1538557	0.80[CEU][hapmap]
rs1555849	0.91[CEU][hapmap]
rs1556916	0.80[CEU][hapmap]
rs1556917	0.80[CEU][hapmap]
rs17034643	0.80[CEU][hapmap]
rs17034821	0.91[CEU][hapmap]
rs17396382	0.95[CEU][hapmap]
rs17400510	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs17401924	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs17401966	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs17410217	0.91[CEU][hapmap]
rs17411502	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2039778	0.80[CEU][hapmap]
rs2182326	0.80[CEU][hapmap]
rs2185252	0.91[CEU][hapmap]
rs2275424	0.95[CEU][hapmap];0.83[JPT][hapmap]
rs35111552	0.82[ASN][1000 genomes]
rs3748577	0.91[CEU][hapmap]
rs3748578	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs3753037	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4240911	0.91[CEU][hapmap]
rs4333852	0.80[CEU][hapmap]
rs4348727	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4475756	0.80[CEU][hapmap]
rs4529713	0.80[CEU][hapmap]
rs4623	0.80[CEU][hapmap]
rs4846197	0.80[CEU][hapmap]
rs4846207	0.80[CEU][hapmap]
rs4846208	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4846209	0.80[CEU][hapmap]
rs4846210	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4846212	0.80[CEU][hapmap]
rs61784566	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61784572	0.81[EUR][1000 genomes]
rs61784573	0.83[ASN][1000 genomes]
rs61784574	0.83[ASN][1000 genomes]
rs61784579	0.83[ASN][1000 genomes]
rs6541089	0.84[CEU][hapmap]
rs6660928	0.85[EUR][1000 genomes]
rs6670208	0.86[EUR][1000 genomes]
rs6670320	0.86[EUR][1000 genomes]
rs6675036	0.86[EUR][1000 genomes]
rs6696056	0.80[CEU][hapmap]
rs6700866	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs746881	0.91[CEU][hapmap]
rs7520935	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs7553228	0.81[CEU][hapmap]
rs8019	0.80[CEU][hapmap]
rs912963	0.80[CEU][hapmap]
rs9332414	0.80[CEU][hapmap]
rs946501	0.80[CEU][hapmap]
rs946503	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv3356570	chr1:10249482-10252272	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv3357571	chr1:10249482-10252272	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12122107	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10231200-10251600	Weak transcription	Right Atrium	heart
2	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
3	chr1:10236400-10258200	Weak transcription	HSMM	muscle
4	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:10241000-10252200	Weak transcription	HepG2	liver
6	chr1:10241000-10252400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:10241000-10254000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:10241000-10254200	Weak transcription	Brain Anterior Caudate	brain
9	chr1:10241000-10254200	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:10241000-10254200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:10241000-10254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:10241000-10257200	Weak transcription	Ovary	ovary
14	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
15	chr1:10241200-10254000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:10241200-10254200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:10241200-10254200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:10241200-10259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:10241400-10253400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:10241400-10255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10241600-10251600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:10241600-10254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:10241600-10254000	Weak transcription	Osteobl	bone
24	chr1:10241800-10254000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:10244200-10256800	Weak transcription	Fetal Stomach	stomach
26	chr1:10247000-10252400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:10247200-10252400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:10247200-10254200	Weak transcription	Fetal Kidney	kidney
29	chr1:10247200-10255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:10248800-10253400	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:10250000-10261000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:10250000-10269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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