Variant report

Variant	rs2180185
Chromosome Location	chr1:10246129-10246130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1002076	0.82[JPT][hapmap]
rs10492969	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10492971	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10492972	0.82[JPT][hapmap]
rs10492973	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10864450	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs10864453	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs11121526	0.90[EUR][1000 genomes]
rs11121551	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs11121555	0.82[JPT][hapmap]
rs11582123	0.82[JPT][hapmap]
rs12120042	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs12120191	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs12127604	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs12130563	0.82[JPT][hapmap]
rs12131441	0.82[JPT][hapmap]
rs12133617	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs12141246	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs12141416	0.82[JPT][hapmap]
rs12737239	0.82[JPT][hapmap]
rs12757288	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1467653	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1536262	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1538557	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1555849	0.82[JPT][hapmap]
rs1556915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1556916	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1556917	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs17034643	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs17034821	0.82[JPT][hapmap]
rs17410217	0.82[JPT][hapmap]
rs1974293	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2027330	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2039778	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2182326	0.84[CEU][hapmap]
rs2185252	0.82[JPT][hapmap]
rs3748575	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs3748577	0.82[JPT][hapmap]
rs3748581	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4240911	0.82[JPT][hapmap]
rs4333852	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4475756	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4529713	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4623	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4845930	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4846196	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4846197	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4846198	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs4846199	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs4846207	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4846209	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs4846212	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs56221672	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6541080	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs6541085	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6541089	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6661326	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667639	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696056	0.84[CEU][hapmap]
rs7418410	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs746881	0.82[JPT][hapmap]
rs7546364	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs7546368	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs7553228	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs7553935	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs8019	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs912962	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs912963	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs9332414	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs946501	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs946503	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs946504	0.84[CEU][hapmap];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2180185	KIF1B	cis	multi-tissue	Pritchard
rs2180185	KIF1B	trans	brain	seeQTL
rs2180185	KIF1B	cis	brain	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10231200-10251600	Weak transcription	Right Atrium	heart
2	chr1:10232800-10246800	Weak transcription	Fetal Kidney	kidney
3	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
4	chr1:10234200-10249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:10236400-10258200	Weak transcription	HSMM	muscle
6	chr1:10240000-10249600	Weak transcription	GM12878-XiMat	blood
7	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:10240200-10246400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:10240200-10246800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:10240400-10246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:10240400-10246400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:10240400-10246600	Weak transcription	Fetal Brain Female	brain
13	chr1:10240400-10246800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:10240400-10250000	Weak transcription	Fetal Brain Male	brain
15	chr1:10241000-10246800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:10241000-10248800	Weak transcription	Brain Angular Gyrus	brain
17	chr1:10241000-10249800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:10241000-10252200	Weak transcription	HepG2	liver
19	chr1:10241000-10252400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:10241000-10254000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:10241000-10254200	Weak transcription	Brain Anterior Caudate	brain
22	chr1:10241000-10254200	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:10241000-10254200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:10241000-10254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:10241000-10257200	Weak transcription	Ovary	ovary
27	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
28	chr1:10241200-10246800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:10241200-10248200	Weak transcription	Right Ventricle	heart
30	chr1:10241200-10248400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:10241200-10248600	Weak transcription	NH-A	brain
32	chr1:10241200-10249000	Weak transcription	Pancreas	Pancrea
33	chr1:10241200-10249400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:10241200-10249600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:10241200-10249800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:10241200-10254000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:10241200-10254200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:10241200-10254200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:10241200-10259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:10241400-10253400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:10241400-10255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:10241600-10246400	Weak transcription	Fetal Intestine Large	intestine
43	chr1:10241600-10246400	Weak transcription	Thymus	Thymus
44	chr1:10241600-10247000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:10241600-10248000	Weak transcription	Esophagus	oesophagus
46	chr1:10241600-10248400	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:10241600-10248400	Weak transcription	Left Ventricle	heart
48	chr1:10241600-10248600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:10241600-10249600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:10241600-10249800	Weak transcription	Monocytes-CD14+_RO01746	blood

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