Variant report

Variant	rs12141201
Chromosome Location	chr1:10454714-10454715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10454620-10454960	HepG2	liver:	n/a	n/a
2	KAP1	chr1:10454320-10454740	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10447080..10448885-chr1:10454434..10456655,2	MCF-7	breast:

Variant related genes	Relation type
PGD	TF binding region

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1002076	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1013952	0.80[EUR][1000 genomes]
rs10492971	0.82[EUR][1000 genomes]
rs10492972	0.89[EUR][1000 genomes]
rs10492973	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1049887	0.89[EUR][1000 genomes]
rs11121537	0.85[EUR][1000 genomes]
rs11121539	0.82[EUR][1000 genomes]
rs11121544	0.81[EUR][1000 genomes]
rs11121545	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11121551	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11121552	0.89[EUR][1000 genomes]
rs11121555	0.93[ASN][1000 genomes]
rs11121557	0.97[ASN][1000 genomes]
rs11121560	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121561	0.93[ASN][1000 genomes]
rs11121563	0.91[ASN][1000 genomes]
rs11121566	0.90[ASN][1000 genomes]
rs1138791	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576384	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11576459	0.82[EUR][1000 genomes]
rs11576654	0.89[EUR][1000 genomes]
rs11576866	0.83[EUR][1000 genomes]
rs11578694	0.87[EUR][1000 genomes]
rs11578788	0.83[EUR][1000 genomes]
rs11579365	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11580789	0.85[EUR][1000 genomes]
rs11582123	0.83[EUR][1000 genomes]
rs11584023	0.83[EUR][1000 genomes]
rs11585760	0.83[EUR][1000 genomes]
rs11585794	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586842	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11587309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587495	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11587854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118323	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12119477	0.83[EUR][1000 genomes]
rs12120042	0.82[EUR][1000 genomes]
rs12120191	0.82[EUR][1000 genomes]
rs12122029	0.82[EUR][1000 genomes]
rs12125535	0.81[EUR][1000 genomes]
rs12127604	0.82[EUR][1000 genomes]
rs12128374	0.86[ASN][1000 genomes]
rs12130563	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12131441	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12132134	0.80[EUR][1000 genomes]
rs12132635	0.84[EUR][1000 genomes]
rs12137880	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12139981	0.85[EUR][1000 genomes]
rs12141246	0.80[EUR][1000 genomes]
rs12141416	0.89[EUR][1000 genomes]
rs12403465	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12409754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409933	0.84[EUR][1000 genomes]
rs12722830	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12725210	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12734551	0.82[EUR][1000 genomes]
rs12737239	0.80[EUR][1000 genomes]
rs12738317	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12746471	0.90[ASN][1000 genomes]
rs12753426	0.80[EUR][1000 genomes]
rs12755363	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1467653	0.83[ASN][1000 genomes]
rs1536262	0.97[ASN][1000 genomes]
rs1555849	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1556916	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1556917	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17034643	0.82[EUR][1000 genomes]
rs17034821	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17401924	0.81[EUR][1000 genomes]
rs17401966	0.82[EUR][1000 genomes]
rs17402762	0.83[ASN][1000 genomes]
rs17410217	0.87[EUR][1000 genomes]
rs17410793	0.83[EUR][1000 genomes]
rs17411502	0.85[EUR][1000 genomes]
rs1889309	0.83[EUR][1000 genomes]
rs2039778	0.82[EUR][1000 genomes]
rs2148152	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182326	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2185252	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2229687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236678	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276100	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34045426	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34075302	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34636442	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35388505	0.90[EUR][1000 genomes]
rs35716098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35759975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35811280	0.96[ASN][1000 genomes]
rs35850116	0.83[EUR][1000 genomes]
rs3737155	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748577	0.89[EUR][1000 genomes]
rs3748578	0.83[EUR][1000 genomes]
rs3748579	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3748581	0.98[ASN][1000 genomes]
rs3762286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762287	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3762288	0.91[ASN][1000 genomes]
rs4240911	0.85[EUR][1000 genomes]
rs4333852	0.84[EUR][1000 genomes]
rs4475756	0.84[EUR][1000 genomes]
rs4623	0.82[EUR][1000 genomes]
rs4845931	0.82[EUR][1000 genomes]
rs4845934	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4846205	0.85[EUR][1000 genomes]
rs4846209	0.81[EUR][1000 genomes]
rs4846212	0.82[EUR][1000 genomes]
rs4846213	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4846216	0.97[ASN][1000 genomes]
rs4846218	0.91[ASN][1000 genomes]
rs4846219	0.91[ASN][1000 genomes]
rs4846221	0.90[ASN][1000 genomes]
rs58014725	0.90[ASN][1000 genomes]
rs58053556	0.88[EUR][1000 genomes]
rs58697740	0.83[EUR][1000 genomes]
rs60743860	0.89[EUR][1000 genomes]
rs61326491	0.86[ASN][1000 genomes]
rs61778376	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61778399	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61778401	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61778402	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61778403	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61778404	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6541089	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6541094	0.89[ASN][1000 genomes]
rs6674843	0.88[EUR][1000 genomes]
rs6674949	0.97[ASN][1000 genomes]
rs6682868	0.97[ASN][1000 genomes]
rs746881	0.89[EUR][1000 genomes]
rs7524693	0.82[EUR][1000 genomes]
rs7530167	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7546364	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7546368	0.83[ASN][1000 genomes]
rs7553228	0.82[EUR][1000 genomes]
rs7553935	0.81[EUR][1000 genomes]
rs912961	0.89[EUR][1000 genomes]
rs912963	0.82[EUR][1000 genomes]
rs9332414	0.81[EUR][1000 genomes]
rs9651117	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv8213	chr1:10450914-10460439	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12141201	KIF1B	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10438600-10458200	Weak transcription	Right Atrium	heart
2	chr1:10439600-10458200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:10440000-10458400	Weak transcription	Lung	lung
4	chr1:10444800-10458200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:10447800-10458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:10448200-10458200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:10448200-10458200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:10448200-10458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:10448600-10454800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:10448600-10458200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:10448600-10458200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:10448600-10458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:10448600-10458400	Weak transcription	HSMM	muscle
14	chr1:10448800-10458200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:10448800-10458200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:10448800-10458200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:10448800-10458200	Weak transcription	HUVEC	blood vessel
18	chr1:10448800-10458200	Weak transcription	NH-A	brain
19	chr1:10448800-10458200	Weak transcription	NHEK	skin
20	chr1:10449000-10458200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:10449000-10458200	Weak transcription	Brain Anterior Caudate	brain
22	chr1:10449000-10458200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:10449000-10458200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:10449000-10458200	Weak transcription	Thymus	Thymus
25	chr1:10449000-10458200	Weak transcription	HSMMtube	muscle
26	chr1:10449200-10458200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:10449200-10458200	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:10449200-10458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:10449600-10457400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:10449600-10458200	Weak transcription	Esophagus	oesophagus
31	chr1:10449600-10458200	Weak transcription	Pancreas	Pancrea
32	chr1:10449600-10458200	Weak transcription	Hela-S3	cervix
33	chr1:10450200-10457200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:10451200-10458000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:10451800-10457200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:10453400-10457600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:10453600-10456200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:10453800-10454800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr1:10453800-10454800	ZNF genes & repeats	A549	lung
40	chr1:10453800-10458200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:10454000-10454800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:10454400-10454800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr1:10454400-10458200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:10454600-10457400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:10454600-10458000	Weak transcription	Brain Substantia Nigra	brain

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