Variant report

Variant	rs12144978
Chromosome Location	chr1:154850445-154850446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154848210..154851147-chr1:154969290..154972007,2	K562	blood:
2	chr1:154642183..154644763-chr1:154849809..154851514,2	MCF-7	breast:
3	chr1:154849815..154852371-chr1:154881627..154884570,2	MCF-7	breast:
4	chr1:154843876..154848485-chr1:154848730..154854790,7	K562	blood:
5	chr1:154850056..154852682-chr1:154903933..154905463,2	MCF-7	breast:
6	chr1:154844363..154847365-chr1:154847993..154851967,4	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1007170	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10796934	0.81[ASN][1000 genomes]
rs10908445	0.81[ASN][1000 genomes]
rs10908447	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10908448	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264276	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11264281	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264284	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12036859	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12069356	0.81[ASN][1000 genomes]
rs12095061	0.84[CEU][hapmap]
rs12130132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1580943	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2061690	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2102423	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2135219	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2174507	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2335407	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2335408	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2335409	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs3738026	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4578216	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4845399	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845677	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845679	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845681	0.85[EUR][1000 genomes]
rs4845683	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4845690	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845691	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845693	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58629129	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6674853	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6699043	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6699080	0.82[EUR][1000 genomes]
rs705094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72702224	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7531728	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7544528	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7553195	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs869506	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs877343	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883718	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs906593	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	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
8	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
rs12144978	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154843200-154850800	Weak transcription	Ovary	ovary
2	chr1:154843200-154854200	Weak transcription	Fetal Kidney	kidney
3	chr1:154843200-154854200	Weak transcription	Right Atrium	heart
4	chr1:154844400-154850800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:154848200-154851200	Enhancers	Pancreas	Pancrea
6	chr1:154849400-154850600	Enhancers	Fetal Intestine Large	intestine
7	chr1:154849400-154850600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:154849400-154850600	Enhancers	Stomach Mucosa	stomach
9	chr1:154849400-154850600	Enhancers	HUVEC	blood vessel
10	chr1:154849400-154851000	Enhancers	Liver	Liver
11	chr1:154849400-154851200	Enhancers	Fetal Intestine Small	intestine
12	chr1:154849600-154850600	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:154849600-154850600	Enhancers	Hela-S3	cervix
14	chr1:154849600-154850600	Flanking Active TSS	HepG2	liver
15	chr1:154849600-154851000	Enhancers	Brain Anterior Caudate	brain
16	chr1:154849600-154851200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:154849600-154851200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:154849600-154851200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:154849600-154851200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:154849800-154850600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:154849800-154851800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:154850000-154850800	Weak transcription	Brain Substantia Nigra	brain
23	chr1:154850000-154851200	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:154850200-154850600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:154850200-154851800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:154850200-154851800	Enhancers	Fetal Brain Female	brain
27	chr1:154850200-154852800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:154850400-154850600	Enhancers	A549	lung
29	chr1:154850400-154851200	Enhancers	Colonic Mucosa	Colon
30	chr1:154850400-154851400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:154850400-154851400	Enhancers	Brain Angular Gyrus	brain
32	chr1:154850400-154851800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:154850400-154853800	Weak transcription	K562	blood
34	chr1:154850400-154857800	Weak transcription	Lung	lung

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