Variant report

Variant	rs444264
Chromosome Location	chr3:139212730-139212731
allele	C/T
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	JUND	chr3:139212712-139213056	HepG2	liver:	n/a	n/a
2	MYC	chr3:139212716-139212821	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:139212683-139213352	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000263538	TF binding region

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1017469	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1080371	0.82[MEX][hapmap]
rs10935321	0.81[AMR][1000 genomes]
rs10935322	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10935326	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10935328	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11705700	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11706576	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11717119	0.84[AMR][1000 genomes]
rs11721246	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11920890	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11928377	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12495890	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13064670	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13313904	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13316469	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13326837	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs13327001	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13327467	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs13434189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1371338	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1371339	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1550352	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1583743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1586862	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1609483	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs167187	0.82[MEX][hapmap]
rs17395255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17395262	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17395304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs176984	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1817830	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1817831	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs188421	0.82[MEX][hapmap]
rs188422	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs192687	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs211582	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs211585	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2118980	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289347	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289349	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2349058	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28771131	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28780368	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28829348	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28861812	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs295472	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs295480	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295483	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295486	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295488	0.90[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34680708	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3555	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35674260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3772881	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs387987	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3888890	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4302343	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4428138	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4547659	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4563370	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4683464	0.86[MEX][hapmap]
rs4683608	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62270814	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62270815	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62270816	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6439858	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6439860	0.82[MEX][hapmap]
rs6439861	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6439862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6771831	0.82[MEX][hapmap]
rs6778992	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6782957	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6801875	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6804877	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7372124	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7372551	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7372811	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs7372813	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7373116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs7373657	0.84[AMR][1000 genomes]
rs7374065	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7374317	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs7374348	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7433335	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7612112	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7616025	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7626658	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7627718	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7645307	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7833	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs878535	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9289574	0.84[AMR][1000 genomes]
rs9289579	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs964226	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs978835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9812991	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9813503	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9817963	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819368	1.00[CEU][hapmap]
rs9821875	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9821891	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs9828954	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9831144	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9833460	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9839681	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9848820	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9848959	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9849255	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9850987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9851318	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs9857390	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9859393	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9859864	0.81[MEX][hapmap]
rs9868900	0.84[AMR][1000 genomes]
rs9869745	0.84[AMR][1000 genomes]
rs9871030	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9872749	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9873011	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9874227	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876640	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9879594	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9881973	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9990108	0.86[AMR][1000 genomes];0.86[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs444264	MRPS22	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208000-139215400	Weak transcription	Fetal Kidney	kidney
2	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:139209200-139213000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:139210200-139212800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:139210400-139212800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:139210400-139212800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:139210400-139217200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:139210600-139212800	Weak transcription	Ovary	ovary
9	chr3:139210800-139215000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:139211000-139212800	Weak transcription	Pancreas	Pancrea
11	chr3:139211400-139213200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:139211400-139213200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:139211800-139214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:139212600-139213000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr3:139212600-139213200	ZNF genes & repeats	Fetal Stomach	stomach
16	chr3:139212600-139213200	Strong transcription	Gastric	stomach
17	chr3:139212600-139213400	Strong transcription	Brain Substantia Nigra	brain
18	chr3:139212600-139213400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
19	chr3:139212600-139213600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:139212600-139213600	ZNF genes & repeats	Esophagus	oesophagus
21	chr3:139212600-139213800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:139212600-139213800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:139212600-139213800	ZNF genes & repeats	Spleen	Spleen

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