Variant report

Variant	rs1049887
Chromosome Location	chr1:10460485-10460486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10457490..10461716-chr1:10469511..10473951,6	K562	blood:
2	chr1:10446399..10450088-chr1:10457513..10461303,7	MCF-7	breast:
3	chr1:10457403..10461622-chr1:10531171..10536559,7	K562	blood:
4	chr1:10457797..10461098-chr1:10474071..10478087,9	K562	blood:
5	chr1:10446950..10451985-chr1:10457311..10462205,6	K562	blood:
6	chr1:10269508..10272201-chr1:10459062..10462119,3	K562	blood:
7	chr1:10446221..10450110-chr1:10457451..10462205,13	MCF-7	breast:
8	chr1:10001846..10004168-chr1:10458912..10460649,2	K562	blood:
9	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
10	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271989	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000054523	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000265945	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1002076	0.89[EUR][1000 genomes]
rs11121533	0.83[EUR][1000 genomes]
rs11121544	0.90[EUR][1000 genomes]
rs11121545	0.84[EUR][1000 genomes]
rs11121551	0.81[EUR][1000 genomes]
rs11121552	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11121560	0.89[EUR][1000 genomes]
rs1138791	0.80[EUR][1000 genomes]
rs11576384	0.84[EUR][1000 genomes]
rs11576654	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576866	0.92[EUR][1000 genomes]
rs11578694	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11578788	0.92[EUR][1000 genomes]
rs11585760	0.92[EUR][1000 genomes]
rs11585794	0.87[EUR][1000 genomes]
rs11587309	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11587495	0.88[EUR][1000 genomes]
rs11587854	0.89[EUR][1000 genomes]
rs12118323	0.85[EUR][1000 genomes]
rs12119477	0.92[EUR][1000 genomes]
rs12130220	0.88[EUR][1000 genomes]
rs12130563	0.85[EUR][1000 genomes]
rs12131441	0.85[EUR][1000 genomes]
rs12132635	0.93[EUR][1000 genomes]
rs12136376	0.82[EUR][1000 genomes]
rs12137456	0.85[EUR][1000 genomes]
rs12137880	0.83[EUR][1000 genomes]
rs12141201	0.89[EUR][1000 genomes]
rs12402052	0.85[EUR][1000 genomes]
rs12403443	0.83[EUR][1000 genomes]
rs12406776	0.82[EUR][1000 genomes]
rs12407992	0.85[EUR][1000 genomes]
rs12408019	0.85[EUR][1000 genomes]
rs12409754	0.89[EUR][1000 genomes]
rs12722830	0.84[EUR][1000 genomes]
rs12734068	0.88[EUR][1000 genomes]
rs12734551	0.91[EUR][1000 genomes]
rs12755094	0.85[EUR][1000 genomes]
rs12755363	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12759696	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1339458	0.87[EUR][1000 genomes]
rs1536263	0.87[EUR][1000 genomes]
rs1555849	0.84[EUR][1000 genomes]
rs17034821	0.84[EUR][1000 genomes]
rs17400510	0.83[EUR][1000 genomes]
rs17401924	0.90[EUR][1000 genomes]
rs17401966	0.91[EUR][1000 genomes]
rs17410793	0.92[EUR][1000 genomes]
rs17411502	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889309	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2004034	0.89[EUR][1000 genomes]
rs2185252	0.84[EUR][1000 genomes]
rs2229687	0.84[EUR][1000 genomes]
rs2236678	0.84[EUR][1000 genomes]
rs2275424	0.87[EUR][1000 genomes]
rs2276100	0.84[EUR][1000 genomes]
rs34045426	0.83[EUR][1000 genomes]
rs34075302	0.81[EUR][1000 genomes]
rs34215045	0.88[EUR][1000 genomes]
rs34225619	0.86[EUR][1000 genomes]
rs35388505	0.81[EUR][1000 genomes]
rs35716098	0.85[EUR][1000 genomes]
rs35766535	0.83[EUR][1000 genomes]
rs35837142	0.86[EUR][1000 genomes]
rs3737155	0.89[EUR][1000 genomes]
rs3748578	0.92[EUR][1000 genomes]
rs3748579	0.84[EUR][1000 genomes]
rs3753037	0.87[EUR][1000 genomes]
rs3762286	0.84[EUR][1000 genomes]
rs4259656	0.84[EUR][1000 genomes]
rs4845933	0.86[EUR][1000 genomes]
rs4845934	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846208	0.85[EUR][1000 genomes]
rs4846210	0.86[EUR][1000 genomes]
rs4846213	0.84[EUR][1000 genomes]
rs58053556	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58549151	0.85[EUR][1000 genomes]
rs58697740	0.92[EUR][1000 genomes]
rs60743860	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61778376	0.84[EUR][1000 genomes]
rs61778399	0.83[EUR][1000 genomes]
rs61778401	0.85[EUR][1000 genomes]
rs61778403	0.83[EUR][1000 genomes]
rs61778404	0.86[EUR][1000 genomes]
rs6674843	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700866	0.83[EUR][1000 genomes]
rs7520651	0.87[EUR][1000 genomes]
rs7520935	0.87[EUR][1000 genomes]
rs7530167	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9651117	0.80[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	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
4	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
5	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
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS 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
rs1049887	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10458200-10460800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:10458200-10460800	Active TSS	HSMMtube	muscle
3	chr1:10458400-10460600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:10458600-10460800	Active TSS	HSMM	muscle
5	chr1:10458600-10461000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:10459200-10460600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr1:10459200-10461200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:10459400-10460800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:10459400-10461000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:10459400-10461200	Active TSS	Right Atrium	heart
11	chr1:10459600-10460600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:10459600-10460600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:10459600-10460600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:10459600-10460600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:10459600-10460600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:10459600-10460600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr1:10459600-10460800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:10459600-10461000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:10459600-10465000	Transcr. at gene 5' and 3'	A549	lung
20	chr1:10459800-10460600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:10459800-10460600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:10459800-10460600	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr1:10459800-10460600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr1:10459800-10460600	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr1:10459800-10460600	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr1:10459800-10460600	Flanking Active TSS	HMEC	breast
27	chr1:10459800-10460600	Flanking Active TSS	NHEK	skin
28	chr1:10459800-10460800	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr1:10459800-10460800	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:10459800-10461000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr1:10459800-10461000	Flanking Active TSS	GM12878-XiMat	blood
32	chr1:10459800-10461000	Flanking Active TSS	NH-A	brain
33	chr1:10459800-10461200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:10459800-10461200	Flanking Active TSS	Liver	Liver
35	chr1:10460000-10460600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:10460000-10460600	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr1:10460000-10460600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:10460000-10460600	Enhancers	Small Intestine	intestine
39	chr1:10460000-10460800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:10460000-10460800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:10460000-10460800	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr1:10460000-10461000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
43	chr1:10460000-10461000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:10460000-10461000	Enhancers	Placenta	Placenta
45	chr1:10460000-10461000	Flanking Active TSS	Hela-S3	cervix
46	chr1:10460000-10461000	Flanking Active TSS	Osteobl	bone
47	chr1:10460000-10461400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:10460000-10461600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
49	chr1:10460000-10461800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:10460000-10463800	Weak transcription	Placenta Amnion	Placenta Amnion

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