Variant report

Variant	rs12127553
Chromosome Location	chr1:10298601-10298602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10298304..10299209-chr3:122134645..122135581,2	NB4	blood:
2	chr1:10276579..10278410-chr1:10297316..10299169,2	K562	blood:
3	chr1:10268925..10271698-chr1:10297795..10299727,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction
ENSG00000196981	Chromatin interaction
ENSG00000272758	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1013952	0.87[EUR][1000 genomes]
rs1013953	0.83[EUR][1000 genomes]
rs10492971	0.84[EUR][1000 genomes]
rs10492973	0.80[EUR][1000 genomes]
rs10864449	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11121528	0.81[ASN][1000 genomes]
rs11121531	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121532	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11121533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121535	0.83[EUR][1000 genomes]
rs11121544	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11576459	0.84[EUR][1000 genomes]
rs11576866	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11578788	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11580854	0.88[EUR][1000 genomes]
rs11582123	0.81[EUR][1000 genomes]
rs11584023	0.80[EUR][1000 genomes]
rs11585760	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12117635	0.84[EUR][1000 genomes]
rs12117765	0.81[ASN][1000 genomes]
rs12119477	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12120042	0.85[EUR][1000 genomes]
rs12120191	0.85[EUR][1000 genomes]
rs12122029	0.84[EUR][1000 genomes]
rs12125535	0.84[EUR][1000 genomes]
rs12127604	0.85[EUR][1000 genomes]
rs12129035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12130220	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132635	0.83[EUR][1000 genomes]
rs12133125	0.85[ASN][1000 genomes]
rs12136376	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137456	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139981	0.80[EUR][1000 genomes]
rs12141246	0.83[EUR][1000 genomes]
rs12402052	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403443	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12406776	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406943	0.87[EUR][1000 genomes]
rs12407992	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408019	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409137	0.87[EUR][1000 genomes]
rs12734068	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12734551	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12737239	0.83[EUR][1000 genomes]
rs12753426	0.81[EUR][1000 genomes]
rs12755094	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757288	0.84[EUR][1000 genomes]
rs12757820	0.81[ASN][1000 genomes]
rs1339458	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536263	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538557	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1556916	0.80[EUR][1000 genomes]
rs17034643	0.85[EUR][1000 genomes]
rs17400510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17401924	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17401966	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17410793	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004034	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2039778	0.85[EUR][1000 genomes]
rs2105212	0.85[EUR][1000 genomes]
rs2182326	0.82[EUR][1000 genomes]
rs2275424	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34215045	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34225619	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34565762	0.89[EUR][1000 genomes]
rs35111552	0.82[ASN][1000 genomes]
rs35187325	0.84[ASN][1000 genomes]
rs35766535	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35830240	0.85[ASN][1000 genomes]
rs35837142	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35850116	0.81[EUR][1000 genomes]
rs3748578	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3753037	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4259656	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4333852	0.82[EUR][1000 genomes]
rs4348727	0.81[ASN][1000 genomes]
rs4475756	0.82[EUR][1000 genomes]
rs4529713	0.87[EUR][1000 genomes]
rs4623	0.85[EUR][1000 genomes]
rs4845931	0.85[EUR][1000 genomes]
rs4845932	0.82[EUR][1000 genomes]
rs4845933	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846197	0.84[EUR][1000 genomes]
rs4846206	0.87[EUR][1000 genomes]
rs4846207	0.87[EUR][1000 genomes]
rs4846208	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846209	0.85[EUR][1000 genomes]
rs4846210	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4846212	0.85[EUR][1000 genomes]
rs55676616	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58549151	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58697740	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61775885	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61775887	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61784573	0.81[ASN][1000 genomes]
rs61784574	0.81[ASN][1000 genomes]
rs61784579	0.81[ASN][1000 genomes]
rs6541089	0.80[EUR][1000 genomes]
rs6685895	0.87[EUR][1000 genomes]
rs6696056	0.87[EUR][1000 genomes]
rs6700866	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520259	0.81[ASN][1000 genomes]
rs7520651	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520935	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524693	0.84[EUR][1000 genomes]
rs7553228	0.85[EUR][1000 genomes]
rs8019	0.80[EUR][1000 genomes]
rs912963	0.85[EUR][1000 genomes]
rs9332414	0.83[EUR][1000 genomes]
rs946501	0.87[EUR][1000 genomes]
rs946502	0.87[EUR][1000 genomes]
rs946503	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv999251	chr1:10276263-10318163	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12127553	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10276800-10311800	Weak transcription	Hela-S3	cervix
3	chr1:10277000-10322000	Weak transcription	Spleen	Spleen
4	chr1:10278400-10302000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:10284800-10311000	Weak transcription	Small Intestine	intestine
6	chr1:10285200-10316000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:10285400-10302400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:10285400-10310800	Weak transcription	Aorta	Aorta
9	chr1:10285400-10312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:10286000-10301800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:10286000-10303000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:10286800-10301600	Weak transcription	Fetal Kidney	kidney
13	chr1:10286800-10305800	Weak transcription	Ovary	ovary
14	chr1:10287400-10312400	Weak transcription	Pancreas	Pancrea
15	chr1:10289000-10300600	Weak transcription	Fetal Heart	heart
16	chr1:10289200-10301600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:10289200-10301800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:10289200-10317400	Weak transcription	Liver	Liver
19	chr1:10290600-10299000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:10291000-10311800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:10291000-10311800	Weak transcription	HMEC	breast
22	chr1:10291200-10311200	Weak transcription	HUVEC	blood vessel
23	chr1:10291400-10308600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:10291800-10299600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:10291800-10300800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:10292000-10301200	Weak transcription	Esophagus	oesophagus
27	chr1:10292400-10299400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:10292400-10299600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:10292400-10309400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:10292600-10299400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:10292600-10303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:10293000-10322000	Weak transcription	Primary T cells from cord blood	blood
33	chr1:10293600-10302800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:10293600-10311400	Weak transcription	NH-A	brain
35	chr1:10293800-10305200	Weak transcription	Fetal Intestine Large	intestine
36	chr1:10294800-10299000	Weak transcription	Right Ventricle	heart
37	chr1:10295000-10310600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:10295400-10311400	Weak transcription	Osteobl	bone
39	chr1:10295600-10302800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:10295600-10312000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:10295600-10316400	Weak transcription	Placenta	Placenta
42	chr1:10295600-10317600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:10295800-10322000	Weak transcription	Lung	lung
44	chr1:10296200-10305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:10296200-10312400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:10296200-10313600	Weak transcription	Fetal Brain Female	brain
47	chr1:10296400-10305200	Weak transcription	Fetal Intestine Small	intestine
48	chr1:10296400-10309800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:10296400-10310600	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:10296400-10312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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