Variant report

Variant	rs62272794
Chromosome Location	chr3:160250880-160250881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160250625..160252912-chr3:160281582..160284023,2	K562	blood:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10212236	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10513551	0.81[AMR][1000 genomes]
rs11918749	0.81[AMR][1000 genomes]
rs13403	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1451761	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1451762	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1451764	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551190	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1584688	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17236544	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17570467	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882126	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1882127	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1920642	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920662	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920664	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279457	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2305407	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2366969	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28705750	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2886825	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732707	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773372	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851366	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4091703	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4292273	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4292274	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4621370	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679654	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679655	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679885	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679888	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679889	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4679890	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679891	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679896	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679899	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679900	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680579	0.81[AMR][1000 genomes]
rs4680580	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4680585	0.85[EUR][1000 genomes]
rs4680587	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4680588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680591	0.80[AMR][1000 genomes]
rs55731730	0.81[AMR][1000 genomes]
rs56156703	0.84[AMR][1000 genomes]
rs56197102	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56394279	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58322641	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60460891	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272800	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272810	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441320	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441324	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768975	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6793560	0.81[AMR][1000 genomes]
rs6798668	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801300	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806505	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808083	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721023	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7611130	0.81[AMR][1000 genomes]
rs7618974	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621724	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7627749	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7627756	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7629	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7629202	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7631792	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7634108	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7634826	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7640072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643779	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644453	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645832	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7647873	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9798898	0.81[AMR][1000 genomes]
rs9862595	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9968151	0.81[AMR][1000 genomes];0.81[EUR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62272794	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:160217200-160254000	Strong transcription	Dnd41	blood
10	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
12	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
13	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
14	chr3:160229000-160253400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:160229200-160252800	Strong transcription	Fetal Thymus	thymus
16	chr3:160229200-160253400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:160229200-160253400	Strong transcription	Osteobl	bone
18	chr3:160229200-160253600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:160229200-160254000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:160229200-160254000	Strong transcription	Placenta	Placenta
21	chr3:160229600-160253400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:160229600-160253600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:160229800-160253200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:160229800-160253400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:160229800-160253600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:160229800-160253600	Strong transcription	HSMM	muscle
27	chr3:160229800-160253800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:160230000-160252800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:160230000-160253000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:160230000-160253600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:160230000-160254000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:160230200-160253600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:160230400-160253000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:160230400-160253200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:160230400-160253400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:160230600-160253400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:160230600-160254600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:160231000-160251000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr3:160231000-160254400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:160234200-160258200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:160234600-160261000	Weak transcription	Spleen	Spleen
42	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
43	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
44	chr3:160236600-160254000	Strong transcription	Hela-S3	cervix
45	chr3:160237400-160253600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:160238200-160253000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr3:160238400-160252800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
49	chr3:160239800-160253400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain

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