Variant report

Variant	rs10908444
Chromosome Location	chr1:154840287-154840288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154837856..154840689-chr1:154908471..154910619,2	MCF-7	breast:
2	chr1:154574246..154575826-chr1:154839450..154841062,2	K562	blood:

Variant related genes	Relation type
ENSG00000160710	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000163344	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1007170	0.83[ASN][1000 genomes]
rs10796934	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10796935	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10908445	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908446	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908447	0.88[ASN][1000 genomes]
rs10908448	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1109815	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11264278	0.84[ASN][1000 genomes]
rs11264281	0.88[ASN][1000 genomes]
rs11264282	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264283	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264284	0.86[ASN][1000 genomes]
rs11264290	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12036859	0.88[ASN][1000 genomes]
rs12069356	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12095061	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12130132	0.83[ASN][1000 genomes]
rs1218582	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12406380	0.83[AMR][1000 genomes]
rs1580943	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1976559	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1977879	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2102423	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2135219	0.88[ASN][1000 genomes]
rs2174507	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2335407	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2335408	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2335409	0.80[ASN][1000 genomes]
rs4240874	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240875	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4339857	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4845398	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845400	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845677	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845678	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845679	0.88[ASN][1000 genomes]
rs4845680	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845681	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4845682	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845683	0.86[ASN][1000 genomes]
rs4845685	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4845687	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845688	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845689	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845690	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845691	0.83[ASN][1000 genomes]
rs4845692	0.81[AMR][1000 genomes]
rs4845693	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4845694	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4845696	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6656435	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656494	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669791	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674853	0.83[ASN][1000 genomes]
rs6683557	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6686873	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6699043	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6699080	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72702224	0.80[ASN][1000 genomes]
rs7528532	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7531728	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544528	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553195	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869506	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs877343	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs883718	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs906593	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9793588	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10908444	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154836400-154840600	Enhancers	Spleen	Spleen
2	chr1:154836400-154841600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
3	chr1:154836600-154840600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:154837200-154842200	Active TSS	Colon Smooth Muscle	Colon
5	chr1:154837800-154840400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:154838400-154842400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:154838600-154841600	Weak transcription	Pancreas	Pancrea
8	chr1:154839000-154840400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:154839000-154840400	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr1:154839000-154840600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:154839000-154840800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
12	chr1:154839200-154840400	Enhancers	Right Ventricle	heart
13	chr1:154839200-154840600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:154839200-154840800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154839200-154840800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:154839200-154840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:154839200-154840800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr1:154839200-154841000	Enhancers	Lung	lung
19	chr1:154839200-154841200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:154839200-154841600	Active TSS	Brain Substantia Nigra	brain
21	chr1:154839200-154842600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr1:154839200-154843000	Active TSS	Brain Angular Gyrus	brain
23	chr1:154839400-154840600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:154839400-154840800	Enhancers	Fetal Heart	heart
25	chr1:154839400-154841200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:154839600-154840400	Active TSS	Brain Hippocampus Middle	brain
27	chr1:154839600-154840400	Weak transcription	Esophagus	oesophagus
28	chr1:154839600-154840600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:154839600-154840600	Active TSS	Brain Anterior Caudate	brain
30	chr1:154839600-154840600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
31	chr1:154839600-154840800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:154839600-154841400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:154839600-154841600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr1:154839600-154842600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:154839800-154840400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:154839800-154840400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:154839800-154840400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:154839800-154840400	Active TSS	Fetal Brain Female	brain
39	chr1:154839800-154840400	Weak transcription	Right Atrium	heart
40	chr1:154839800-154840600	Active TSS	NH-A	brain
41	chr1:154839800-154841000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:154839800-154841000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:154839800-154841000	Enhancers	Left Ventricle	heart
44	chr1:154839800-154841600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
45	chr1:154839800-154843200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:154840000-154840400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:154840000-154840400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr1:154840000-154840400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:154840000-154840400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:154840000-154840400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland

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